4BPU | pdb_00004bpu

Crystal structure of human primase in heterodimeric form, comprising PriS and truncated PriL lacking the C-terminal Fe-S domain.

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e4bpuB1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: RNA_pol_I_A49	F:	ECOD (20:10:01)
D		e4bpuD1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: RNA_pol_I_A49	F:	ECOD (20:10:01)
C		e4bpuC1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: SHMT	F:	ECOD (20:10:01)
A		e4bpuA1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: SHMT	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.20.930.80	Mainly Alpha	Up-down Bundle	Transcription Elongation Factor S-II	Chain A	CATH (4.3.0)
D	1.20.930.80	Mainly Alpha	Up-down Bundle	Transcription Elongation Factor S-II	Chain A	CATH (4.3.0)
C	3.90.920.10	Alpha Beta	Alpha-Beta Complex	DNA primase, PRIM domain	DNA primase, PRIM domain	CATH (4.3.0)
A	3.90.920.10	Alpha Beta	Alpha-Beta Complex	DNA primase, PRIM domain	DNA primase, PRIM domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF26466	Eukaryotic and archaeal DNA primase, large subunit N-terminal domain (DNA_primase_lrg_N)	Eukaryotic and archaeal DNA primase, large subunit N-terminal domain	DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 ( ...	DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast S. cerevisiae) [1]. The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase [4].	Domain
A, C	PF01896	DNA primase small subunit (DNA_primase_S)	DNA primase small subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	DNA PRIMASE LARGE SUBUNIT	DNA binding binding nucleic acid binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding DNA/RNA hybrid binding	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process	membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome nucleoplasm membraneless organelle replication fork catalytic complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome
A, C	DNA PRIMASE SMALL SUBUNIT	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding transition metal ion binding zinc ion binding DNA-directed RNA polymerase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding transition metal ion binding zinc ion binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA replication, synthesis of primer RNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process	membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membrane-bounded organelle protein-containing complex alpha DNA polymerase:primase complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome nucleoplasm membraneless organelle replication fork catalytic complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle DNA polymerase complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen replisome membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR058560	DNA primase, large subunit C-terminal domain, eukaryotic and archaeal	Domain
B, D	IPR016558	DNA primase, large subunit, eukaryotic	Family
B, D	IPR007238	DNA primase large subunit, eukaryotic/archaeal	Family
A, C	IPR002755	DNA primase, small subunit	Family
A, C	IPR014052	DNA primase, small subunit, eukaryotic/archaeal	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: P49643	atypical teratoid rhabdoid tumor heart disease lung cancer medulloblastoma primitive neuroectodermal tumor Gaucher disease large cell medulloblastoma malignant ependymoma non-small cell lung carcinoma psoriasis glioblastoma lung adenocarcinoma malignant glioma osteosarcoma
A, C	Pharos: P49642	adrenal cortex carcinoma large cell medulloblastoma malignant colon neoplasm medulloblastoma Sjogren syndrome atrial fibrillation lung cancer malignant glioma non-small cell lung carcinoma glioblastoma lymphoplasmacytic lymphoma malignant mesothelioma primitive neuroectodermal tumor

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.