2NVU | pdb_00002nvu

Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E [auth J]	d2nvuj_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Nedd8	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth I]	d2nvui_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Nedd8	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2nvuc1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	UBC-related	Ubiquitin conjugating enzyme, UBC	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2nvub2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	D-maltodextrin-binding protein, MBP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2nvub1	Alpha and beta proteins (a/b)	Activating enzymes of the ubiquitin-like proteins	Activating enzymes of the ubiquitin-like proteins	Ubiquitin activating enzymes (UBA)	UBA3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2nvua_	Alpha and beta proteins (a/b)	Activating enzymes of the ubiquitin-like proteins	Activating enzymes of the ubiquitin-like proteins	Ubiquitin activating enzymes (UBA)	Amyloid beta precursor protein-binding protein 1, APPBP1	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)
E [auth J]	SCOP2B Superfamily	Ubiquitin-like	8034470	3000157	SCOP2B (2022-06-29)
D [auth I]	SCOP2B Superfamily	Ubiquitin-like	8034470	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	UBC-like	8034219	3000570	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Duplicated CC (catalytic cysteine) domain-like	8003546	3000141	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003537	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003537	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CC (catalytic cysteine) domain-like	8003548	3000140	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)
E [auth J]	ubiquitin_4	e2nvuJ1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_4	ECOD (1.6)
D [auth I]	ubiquitin_4	e2nvuI1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_4	ECOD (1.6)
C	UQ_con	e2nvuC1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
B	UBA_e1_thiolCys	e2nvuB5	A: alpha arrays	X: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	H: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	T: Catalytic cysteine domain in ubiquitin-activating enzyme	F: UBA_e1_thiolCys	ECOD (1.6)
B	E2_bind	e2nvuB1	A: a+b two layers	X: beta-Grasp	H: E2-binding domain of E1 (From Topology)	T: E2-binding domain of E1	F: E2_bind	ECOD (1.6)
B	ThiF_1	e2nvuB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Activating enzymes of the ubiquitin-like proteins	F: ThiF_1	ECOD (1.6)
B	SBP_bac_1_C	e2nvuB3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
B	SBP_bac_1_N_1	e2nvuB4	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_N_1	ECOD (1.6)
A	ThiF_2,APPBP1_RUB	e2nvuA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Activating enzymes of the ubiquitin-like proteins	F: ThiF_2,APPBP1_RUB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth J]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D [auth I]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	1.10.10.520	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ubiquitin activating enzymes (Uba3). Chain: B, domain 2	CATH (4.3.0)
B	3.10.290.20	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth I], E [auth J]	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
C	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain
B	PF01547	Bacterial extracellular solute-binding protein (SBP_bac_1)	Bacterial extracellular solute-binding protein	-	Family
A	PF00899	ThiF family (ThiF)	ThiF family	This domain is found in ubiquitin activating E1 family and members of the bacterial ThiF/MoeB/HesA family. It is repeated in Ubiquitin-activating enzyme E1 [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth I], E [auth J]	NEDD8	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process localization macromolecule localization intracellular protein localization catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process localization macromolecule localization intracellular protein localization catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of proteolysis regulation of metabolic process post-translational protein modification protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal developmental process anatomical structure morphogenesis anatomical structure development ubiquitin-dependent protein catabolic process multicellular organismal process regulation of cellular component organization cellular component organization cellular component biogenesis multicellular organism development cellular component assembly regulation of postsynapse assembly cell junction assembly regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality system development postsynapse organization postsynapse assembly regulation of postsynapse organization nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen synapse cell junction glutamatergic synapse postsynapse
C	NEDD8-conjugating enzyme Ubc12	binding 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 binding 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 aminoacyltransferase activity ubiquitin-like protein transferase activity NEDD8 transferase activity catalytic activity, acting on a protein acyltransferase activity NEDD8 conjugating enzyme activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process multicellular organismal process regulation of cellular component organization regulation of cellular process cellular component organization cellular component biogenesis multicellular organism development macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process multicellular organismal process regulation of cellular component organization regulation of cellular process cellular component organization cellular component biogenesis multicellular organism development cellular component assembly regulation of postsynapse assembly cell junction assembly anatomical structure development regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality system development developmental process regulation of biological process postsynapse organization postsynapse assembly biological regulation regulation of postsynapse organization nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol presynapse synapse cell junction postsynapse membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol presynapse synapse cell junction postsynapse membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen glutamatergic synapse
B	Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimera	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport response to disaccharide response to oxygen-containing compound detection of maltose stimulus detection of stimulus response to carbohydrate detection of chemical stimulus detection of disaccharide stimulus response to maltose detection of carbohydrate stimulus	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space outer membrane-bounded periplasmic space cell envelope
A	NEDD8-activating enzyme E1 regulatory subunit	protein heterodimerization activity protein binding binding protein dimerization activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding NEDD8 activating enzyme activity ubiquitin-like modifier activating enzyme activity ligase activity, forming carbon-sulfur bonds catalytic activity, acting on a protein catalytic activity ligase activity ATP-dependent activity	cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication mitotic G2/M transition checkpoint regulation of mitotic cell cycle cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication mitotic G2/M transition checkpoint regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle DNA replication checkpoint signaling regulation of cell cycle cell cycle process cell cycle G2/M phase transition regulation of biological process mitotic DNA replication checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition cellular process negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition multicellular organismal process regulation of cellular component organization cellular component organization cellular component biogenesis multicellular organism development cellular component assembly regulation of postsynapse assembly cell junction assembly anatomical structure development regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality system development developmental process postsynapse organization postsynapse assembly regulation of postsynapse organization nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly neuron apoptotic process apoptotic process cell death programmed cell death regulation of apoptotic process regulation of programmed cell death regulation of neuron apoptotic process primary metabolic process macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein-containing complex synapse cell junction glutamatergic synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth I], E [auth J]	IPR019954	Ubiquitin conserved site	Conserved Site
D [auth I], E [auth J]	IPR050158	Ubiquitin and ubiquitin-like	Family
D [auth I], E [auth J]	IPR038738	Nedd8-like ubiquitin	Domain
D [auth I], E [auth J]	IPR000626	Ubiquitin-like domain	Domain
D [auth I], E [auth J]	IPR019956	Ubiquitin domain	Domain
D [auth I], E [auth J]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C	IPR050113	Ubiquitin-conjugating enzyme	Family
C	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
C	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
C	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
B	IPR006061	Solute-binding family 1, conserved site	Conserved Site
B	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
B	IPR006059	Bacterial-type extracellular solute-binding protein	Family
A	IPR045886	ThiF/MoeB/HesA family	Family
A	IPR030667	NEDD8-activating enzyme E1 regulatory subunit APP-BP1	Family
A	IPR000594	THIF-type NAD/FAD binding fold	Domain
A	IPR035985	Ubiquitin-activating enzyme-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth I], E [auth J]	Pharos: Q15843	language disorder
C	Pharos: P61081	astrocytic tumor dermatomyositis oligodendroglioma psoriasis colorectal adenoma glioblastoma osteosarcoma colorectal cancer lung cancer plasma cell myeloma
A	Pharos: Q13564	lung cancer pancreatic intraductal papillary-mucinous neoplasm medulloblastoma plasma cell myeloma ovarian cancer

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.