3MI9

Crystal structure of HIV-1 Tat complexed with human P-TEFb

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3mi9a_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Cell division protein kinase 9, CDK9	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3mi9b1	All alpha proteins	Cyclin-like	Cyclin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Protein kinase-like (PK-like)	8039362	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cyclin-like	8039367	3000768	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cyclin-like	8039364	3000768	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Pkinase_Tyr	e3mi9A1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
B	KOG0834	e3mi9B3	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: KOG0834	ECOD (1.6)
B	Cyclin_N_1	e3mi9B1	A: alpha arrays	X: HTH	H: HTH	T: Cyclin-like	F: Cyclin_N_1	ECOD (1.6)
C	Tat	e3mi9C1	A: extended segments	X: HIV-1 Tat (From Topology)	H: HIV-1 Tat (From Topology)	T: HIV-1 Tat	F: Tat	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
A	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
B	1.10.472.10	Mainly Alpha	Orthogonal Bundle	Cyclin A	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain	-	Domain
B	PF00134	Cyclin, N-terminal domain (Cyclin_N)	Cyclin, N-terminal domain	Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.	Domain
B	PF21797	Cyclin-T2-like, C-terminal domain (CycT2-like_C)	Cyclin-T2-like, C-terminal domain	This domain is found at the C-terminal end of human Cyclin-T2 (CycT2) and similar animal sequences. CycT2 is the regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P ...	This domain is found at the C-terminal end of human Cyclin-T2 (CycT2) and similar animal sequences. CycT2 is the regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFB). This domain adopts s cyclin box fold consisting of five helices and a short C-terminal helix [2].	Domain
C	PF00539	Transactivating regulatory protein (Tat) (Tat)	Transactivating regulatory protein (Tat)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Cell division protein kinase 9	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding RNA binding snRNA binding 7SK snRNA binding catalytic activity, acting on a protein protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity cyclin-dependent protein serine/threonine kinase activity cyclin-dependent protein kinase activity protein binding kinase binding enzyme binding protein kinase binding transcription factor binding transcription coregulator binding transcription coactivator binding transcription regulator activity transcription elongation factor activity RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA-templated DNA replication maintenance of fidelity metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process replication fork processing nucleic acid metabolic process cellular biosynthetic process RNA metabolic process mRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA-templated DNA replication maintenance of fidelity metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process replication fork processing nucleic acid metabolic process cellular biosynthetic process RNA metabolic process mRNA processing regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA metabolic process RNA 3'-end processing regulation of nucleobase-containing compound metabolic process RNA processing regulation of mRNA processing regulation of biological process cellular metabolic process mRNA 3'-end processing regulation of mRNA 3'-end processing biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process biosynthetic process cellular process regulation of mRNA metabolic process regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II cell population proliferation developmental process regulation of cellular process regulation of developmental process cellular developmental process regulation of cell differentiation muscle cell differentiation muscle structure development regulation of muscle cell differentiation cell differentiation anatomical structure development protein localization regulation of localization cellular localization protein localization to chromatin regulation of protein localization negative regulation of biological process negative regulation of protein localization to chromatin localization protein localization to chromosome regulation of cellular localization cellular macromolecule localization macromolecule localization protein localization to organelle negative regulation of cellular process regulation of protein localization to chromatin negative regulation of protein localization organelle localization nucleus localization DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter viral gene expression biological process involved in interspecies interaction between organisms modulation by host of symbiont process viral process biological process involved in interaction with symbiont viral transcription positive regulation by host of viral transcription biological process involved in symbiotic interaction protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair transcription elongation by RNA polymerase II cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis transcription elongation-coupled chromatin remodeling DNA-templated transcription elongation positive regulation of biological process positive regulation of protein localization positive regulation of protein localization to chromatin positive regulation of cellular process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription elongation by RNA polymerase II regulation of cellular metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process cell cycle regulation of cell cycle regulation of cellular response to stress regulation of response to stress regulation of DNA repair regulation of response to stimulus regulation of DNA metabolic process response to peptide response to chemical response to cytokine cellular response to cytokine stimulus	membrane cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen protein kinase complex intracellular organelle nucleoplasm membrane cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen protein kinase complex intracellular organelle nucleoplasm catalytic complex cyclin/CDK positive transcription elongation factor complex cyclin-dependent protein kinase holoenzyme complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups organelle lumen carboxy-terminal domain protein kinase complex organelle serine/threonine protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex nuclear lumen intracellular non-membrane-bounded organelle cytoplasmic ribonucleoprotein granule cytoplasm supramolecular complex non-membrane-bounded organelle ribonucleoprotein granule P-TEFb complex nuclear body PML body
B	Cyclin-T1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding chromatin binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity RNA polymerase binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding chromatin binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity RNA polymerase binding protein binding enzyme binding RNA binding snRNA binding 7SK snRNA binding cyclin-dependent protein serine/threonine kinase activator activity enzyme regulator activity protein serine/threonine kinase activator activity molecular function activator activity protein kinase regulator activity kinase activator activity enzyme activator activity cyclin-dependent protein serine/threonine kinase regulator activity molecular function regulator activity protein kinase activator activity kinase regulator activity kinase binding protein kinase binding transcription factor binding DNA-binding transcription factor binding	response to stimulus response to chemical response to xenobiotic stimulus regulation of cellular process positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process response to stimulus response to chemical response to xenobiotic stimulus regulation of cellular process positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of biological process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular biosynthetic process cell division transcription by RNA polymerase II viral gene expression biological process involved in interspecies interaction between organisms modulation by host of symbiont process viral process biological process involved in interaction with symbiont viral transcription positive regulation by host of viral transcription biological process involved in symbiotic interaction regulation of transcription by RNA polymerase II regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II transcription elongation by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation regulation of cyclin-dependent protein kinase activity regulation of transferase activity regulation of cyclin-dependent protein serine/threonine kinase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process protein metabolic process cell cycle phosphorus metabolic process protein modification process regulation of cell cycle protein phosphorylation phosphorylation regulation of protein metabolic process regulation of protein kinase activity regulation of molecular function regulation of kinase activity macromolecule modification regulation of protein serine/threonine kinase activity regulation of phosphorylation regulation of phosphorus metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen protein kinase complex intracellular organelle nucleoplasm catalytic complex cyclin/CDK positive transcription elongation factor complex membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen protein kinase complex intracellular organelle nucleoplasm catalytic complex cyclin/CDK positive transcription elongation factor complex cyclin-dependent protein kinase holoenzyme complex intracellular membrane-bounded organelle cellular anatomical entity transferase complex, transferring phosphorus-containing groups organelle lumen carboxy-terminal domain protein kinase complex organelle serine/threonine protein kinase complex nuclear cyclin-dependent protein kinase holoenzyme complex nuclear lumen cytoplasm cytosol P-TEFb complex
C	Protein Tat	protein binding binding protein domain specific binding transcription regulator activity RNA-binding transcription regulator activity enzyme regulator activity phosphatase inhibitor activity molecular function inhibitor activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity protein phosphatase inhibitor activity enzyme inhibitor activity protein serine/threonine phosphatase inhibitor activity protein binding binding protein domain specific binding transcription regulator activity RNA-binding transcription regulator activity enzyme regulator activity phosphatase inhibitor activity molecular function inhibitor activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity protein phosphatase inhibitor activity enzyme inhibitor activity protein serine/threonine phosphatase inhibitor activity cyclin binding cytoskeletal protein binding actinin binding RNA binding trans-activation response element binding organic cyclic compound binding nucleic acid binding pre-miRNA binding molecular sequestering activity cation binding ion binding metal ion binding small molecule binding	symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host translation biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host gene expression symbiont-mediated suppression of host translation initiation symbiont-mediated perturbation of host process symbiont-mediated suppression of host translation symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism regulation of cellular process regulation of protein modification process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host translation biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host gene expression symbiont-mediated suppression of host translation initiation symbiont-mediated perturbation of host process symbiont-mediated suppression of host translation symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism regulation of cellular process regulation of protein modification process regulation of protein phosphorylation negative regulation of biological process regulation of peptidyl-threonine phosphorylation negative regulation of phosphate metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process negative regulation of cellular process peptidyl-amino acid modification protein metabolic process peptidyl-threonine modification protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process protein phosphorylation phosphorylation regulation of protein metabolic process cellular metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of peptidyl-threonine phosphorylation negative regulation of phosphorus metabolic process metabolic process regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process negative regulation of phosphorylation regulation of metabolic process peptidyl-threonine phosphorylation apoptotic process cell death programmed cell death cellular biosynthetic process RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process modulation by virus of host process modulation by virus of host chromatin organization cellular component organization chromatin organization viral process cellular component organization or biogenesis symbiont-mediated perturbation of host defense response response to host defenses response to stimulus response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism response to external stimulus response to biotic stimulus evasion of host immune response response to host immune response response to host response to external biotic stimulus virus-mediated perturbation of host defense response modulation by virus of host cellular process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular biosynthetic process DNA-templated transcription elongation positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process symbiont-mediated perturbation of host defenses symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated perturbation of host signal transduction pathway viral gene expression regulation of viral process regulation of viral transcription positive regulation of viral process viral transcription positive regulation of viral transcription	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell part host intracellular region cellular anatomical entity host cell nucleus host cell nucleolus host cell nuclear part host intracellular organelle host cell cytoplasm extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR000719	Protein kinase domain	Domain
A	IPR050108	Cyclin-dependent kinase	Family
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR008271	Serine/threonine-protein kinase, active site	Active Site
B	IPR047320	Cyclin-T1, second cyclin box	Domain
B	IPR006671	Cyclin, N-terminal	Domain
B	IPR036915	Cyclin-like superfamily	Homologous Superfamily
B	IPR043198	Cyclin/Cyclin-like subunit Ssn8	Family
B	IPR013763	Cyclin-like domain	Domain
C	IPR001831	Immunodeficiency virus transactivating regulatory protein (Tat)	Family
C	IPR036963	Tat domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P50750	Gaucher disease
B	Pharos: O60563	acute myeloid leukemia osteosarcoma Pick disease juvenile dermatomyositis ovarian cancer psoriasis myopathy pancreatic ductal adenocarcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.