7E15 | pdb_00007e15

Protein ternary complex working for DNA replication initiation

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Ion_trans, Ion_trans_2	e7e15F1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: CNF1/YfiH-like putative cysteine hydrolases	T: CNF1/YfiH-like putative cysteine hydrolases	F: Ion_trans, Ion_trans_2	ECOD (v294.1)
C	Ion_trans, Ion_trans_2	e7e15C1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: CNF1/YfiH-like putative cysteine hydrolases	T: CNF1/YfiH-like putative cysteine hydrolases	F: Ion_trans, Ion_trans_2	ECOD (v294.1)
E	Ion_trans, Ion_trans_2	e7e15E1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: CNF1/YfiH-like putative cysteine hydrolases	T: CNF1/YfiH-like putative cysteine hydrolases	F: Ion_trans, Ion_trans_2	ECOD (v294.1)
B	Ion_trans, Ion_trans_2	e7e15B1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: CNF1/YfiH-like putative cysteine hydrolases	T: CNF1/YfiH-like putative cysteine hydrolases	F: Ion_trans, Ion_trans_2	ECOD (v294.1)
D	Glyco_transf_41	e7e15D1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (v294.1)
A	Glyco_transf_41	e7e15A1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.1640.30	Alpha Beta	Alpha-Beta Complex	inorganic pyrophosphatase (n-terminal core)		CATH (utative)
D	3.10.310.30	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (utative)
A	3.90.1640.30	Alpha Beta	Alpha-Beta Complex	inorganic pyrophosphatase (n-terminal core)		CATH (utative)
A	3.10.310.30	Alpha Beta	Roll	Diaminopimelate Epimerase	Chain A, domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF22317	DNA polymerase II small subunit, N-terminal domain (PolB_N)	DNA polymerase II small subunit, N-terminal domain	This domain is found at the N-terminal end of DNA polymerase II small subunit from Pyrococcus horikoshii (PolB) and similar archaeal sequences. PolB possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades s ...	This domain is found at the N-terminal end of DNA polymerase II small subunit from Pyrococcus horikoshii (PolB) and similar archaeal sequences. PolB possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single -stranded DNA in the 3' to 5' direction. This domain folds into a four alpha-helix bundle that includes a short parallel beta -sheet [1].	Domain
B, E	PF22090	Gins51, C-terminal domain (Gins51_C)	Gins51, C-terminal domain	This domain is found at the C-terminal end of the DNA replication complex GINS family protein TK0536 from Thermococcus kodakarensis (Gins51, Swiss:Q5JF31). This mobile domain acts as a hook to bind the archaeal GINS-associated nuclease to form the 'C ...	This domain is found at the C-terminal end of the DNA replication complex GINS family protein TK0536 from Thermococcus kodakarensis (Gins51, Swiss:Q5JF31). This mobile domain acts as a hook to bind the archaeal GINS-associated nuclease to form the 'CGM' unwindosome complex. It shows an alpha-beta configuration [1,2].	Domain
A, D	PF21763	DHH-CID domain (DHH_CID)	DHH-CID domain	DHH-CID (CMG Interacting Domain) domain is found in proteins that are members of DHH phosphatase family. This domain is located between the catalytic domains and consists of array of four helices with two 'kissing' loops. The DHH-CID domain contains ...	DHH-CID (CMG Interacting Domain) domain is found in proteins that are members of DHH phosphatase family. This domain is located between the catalytic domains and consists of array of four helices with two 'kissing' loops. The DHH-CID domain contains H2TH motif and is structurally very similar to proteins members of S13-like H2TH superfamily.	Domain
A, D	PF02272	DHHA1 domain (DHHA1)	DHHA1 domain	This domain is often found adjacent to the DHH domain Pfam:PF01368 and is called DHHA1 for DHH associated domain. This domain is diagnostic of DHH subfamily 1 members [1]. This domain is also found in alanyl tRNA synthetase e.g. Swiss:P00957, suggest ...	This domain is often found adjacent to the DHH domain Pfam:PF01368 and is called DHHA1 for DHH associated domain. This domain is diagnostic of DHH subfamily 1 members [1]. This domain is also found in alanyl tRNA synthetase e.g. Swiss:P00957, suggesting that this domain may have an RNA binding function. The domain is about 60 residues long and contains a conserved GG motif.	Domain
A, D	PF01368	DHH family, N-terminal domain (DHH)	DHH family, N-terminal domain	It is predicted that this family of proteins all perform a phosphoesterase function. This domain is found at the N-terminal of the single stranded DNA exonuclease RecJ. It shows an alpha-beta configuration [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	DNA polymerase II small subunit	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity	catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process DNA-templated DNA replication DNA strand elongation catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process DNA-templated DNA replication DNA strand elongation DNA replication DNA strand elongation involved in DNA replication	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex DNA polymerase complex intracellular protein-containing complex
B, E	Gins51	-	-	-
A, D	SsDNA-specific exonuclease	binding nucleic acid binding single-stranded DNA 5'-3' DNA exonuclease activity DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds binding nucleic acid binding single-stranded DNA 5'-3' DNA exonuclease activity DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity	nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR007185	DNA polymerase alpha/delta/epsilon, subunit B	Domain
C, F	IPR054750	DNA polymerase II small subunit, N-terminal domain	Domain
C, F	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
C, F	IPR011149	DNA polymerase II small subunit, archaeal	Family
C, F	IPR024826	DNA polymerase delta/II small subunit family	Family
C, F	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
B, E	IPR016745	Archaeal GINS complex, Gins51 subunit	Family
B, E	IPR054314	Gins51, C-terminal domain	Domain
A, D	IPR001667	DDH domain	Domain
A, D	IPR048515	DHH-CID domain	Domain
A, D	IPR038763	DHH phosphoesterase superfamily	Homologous Superfamily
A, D	IPR003156	DHHA1 domain	Domain
A, D	IPR051673	Single-stranded-DNA-specific exonuclease RecJ	Family

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.