3U61 | pdb_00003u61

Structure of T4 Bacteriophage Clamp Loader Bound To Closed Clamp, DNA and ATP Analog and ADP

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth A]	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8092970	3000691	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	DNA clamp	8036422	3000780	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 [auth B]	SBP_bac_1	e3u61B1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: SBP_bac_1	ECOD (v294.1)
A [auth B]	tRNA-synt_1_2	e3u61B4	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (v294.1)
A [auth B]	Nup54_57_C	e3u61B2	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Nup54_57_C	ECOD (v294.1)
B [auth C]	SBP_bac_1	e3u61C2	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: SBP_bac_1	ECOD (v294.1)
B [auth C]	tRNA-synt_1_2	e3u61C3	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (v294.1)
B [auth C]	Nup54_57_C	e3u61C4	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Nup54_57_C	ECOD (v294.1)
C [auth D]		e3u61D2	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F:	ECOD (v294.1)
C [auth D]	tRNA-synt_1_2	e3u61D4	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (v294.1)
C [auth D]	Nup54_57_C	e3u61D3	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Nup54_57_C	ECOD (v294.1)
D [auth E]	NAGLU_N	e3u61E1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: NAGLU_N	ECOD (v294.1)
E [auth A]	Tae4	e3u61A1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: Tae4	ECOD (v294.1)
F [auth G]	PUF	e3u61G1	A: a/b three-layered sandwiches	X: Insertion subdomain in DsbA-like	H: Insertion subdomain in DsbA-like	T: Insertion subdomain in DsbA-like	F: PUF	ECOD (v294.1)
G [auth H]	PUF	e3u61H1	A: a/b three-layered sandwiches	X: Insertion subdomain in DsbA-like	H: Insertion subdomain in DsbA-like	T: Insertion subdomain in DsbA-like	F: PUF	ECOD (v294.1)
H [auth F]	PUF	e3u61F1	A: a/b three-layered sandwiches	X: Insertion subdomain in DsbA-like	H: Insertion subdomain in DsbA-like	T: Insertion subdomain in DsbA-like	F: PUF	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A [auth B]	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A [auth B]	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)
B [auth C]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B [auth C]	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B [auth C]	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)
C [auth D]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C [auth D]	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C [auth D]	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)
D [auth E]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D [auth E]	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D [auth E]	1.20.272.10	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)
E [auth A]	6.10.250.1260	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
E [auth A]	1.20.272.50	Mainly Alpha	Up-down Bundle	Zinc Finger, Delta Prime	domain 3	CATH (4.3.0)
E [auth A]	1.10.8.700	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
F [auth G]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
G [auth H]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
H [auth F]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth C], C [auth D], D [auth E]	PF21328	Sliding-clamp-loader large subunit, AAA+ ATPase lid domain (Gp44_lid)	Sliding-clamp-loader large subunit, AAA+ ATPase lid domain	Sliding-clamp-loader large subunit (also known as Gp44) from Bacteriophage T4 forms the sliding-clamp-loader together with the small subunit. These are members of the AAA+ superfamily of ATPases which form pentameric complexes that load sliding DNA c ...	Sliding-clamp-loader large subunit (also known as Gp44) from Bacteriophage T4 forms the sliding-clamp-loader together with the small subunit. These are members of the AAA+ superfamily of ATPases which form pentameric complexes that load sliding DNA clamps onto the DNA, key for processive chromosomal replication [1,2]. This entry represents the AAA+ ATPase lid domain.	Domain
A [auth B], B [auth C], C [auth D], D [auth E]	PF21429	Sliding-clamp-loader large subunit, C-terminal domain (Gp44_C)	Sliding-clamp-loader large subunit, C-terminal domain	This domain is found at the C-terminal end of Sliding-clamp-loader large subunit from Bacteriophage T4 (Gp44) and similar proteins predominantly found in tailed bacteriophages. Gp44 functions as an ATPase enzyme. It also contains an AAA module (Pfam: ...	This domain is found at the C-terminal end of Sliding-clamp-loader large subunit from Bacteriophage T4 (Gp44) and similar proteins predominantly found in tailed bacteriophages. Gp44 functions as an ATPase enzyme. It also contains an AAA module (Pfam:PF00004) [1,2].	Domain
A [auth B], B [auth C], C [auth D], D [auth E]	PF00004	ATPase family associated with various cellular activities (AAA) (AAA)	ATPase family associated with various cellular activities (AAA)	AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].	Domain
E [auth A]	PF16790	Bacteriophage clamp loader A subunit (Phage_clamp_A)	Bacteriophage clamp loader A subunit	This is the A subunit of bacteriophage DNA clamp loader required for loading of sliding clamps onto chromosomal DNA. These clamps are involved in processivity of DNA replication [1].	Domain
F [auth G], G [auth H], H [auth F]	PF09116	gp45 sliding clamp, C terminal (gp45-slide_C)	gp45 sliding clamp, C terminal	Members of this family are essential for the interaction of the gp45 sliding clamp with the corresponding polymerase. They adopt a DNA clamp fold, consisting of two alpha helices and two beta sheets - the fold is duplicated and has internal pseudo tw ...	Members of this family are essential for the interaction of the gp45 sliding clamp with the corresponding polymerase. They adopt a DNA clamp fold, consisting of two alpha helices and two beta sheets - the fold is duplicated and has internal pseudo two-fold symmetry [1].	Domain
F [auth G], G [auth H], H [auth F]	PF02916	DNA polymerase processivity factor (DNA_PPF)	DNA polymerase processivity factor		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth C], C [auth D], D [auth E]	DNA polymerase accessory protein 44	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 DNA binding nucleic acid binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA clamp loader activity catalytic activity ATP-dependent activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process bidirectional double-stranded viral DNA replication metabolic process viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process bidirectional double-stranded viral DNA replication metabolic process cellular process macromolecule metabolic process DNA biosynthetic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair DNA-templated DNA replication DNA replication	-
E [auth A]	DNA polymerase accessory protein 62	DNA binding binding nucleic acid binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA clamp loader activity catalytic activity ATP-dependent activity	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process bidirectional double-stranded viral DNA replication DNA biosynthetic process	-
F [auth G], G [auth H], H [auth F]	DNA polymerase processivity component	enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral gene expression viral process viral transcription viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral gene expression viral process viral transcription viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process viral genome replication bidirectional double-stranded viral DNA replication DNA biosynthetic process	-
I	Template DNA strand	-	-	-
J	Primer DNA strand	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth C], C [auth D], D [auth E]	IPR050238	DNA Replication and Repair Clamp Loader Complex	Family
A [auth B], B [auth C], C [auth D], D [auth E]	IPR046388	Sliding-clamp-loader large subunit	Family
A [auth B], B [auth C], C [auth D], D [auth E]	IPR048815	Sliding-clamp-loader large subunit, AAA+ ATPase lid domain	Domain
A [auth B], B [auth C], C [auth D], D [auth E]	IPR048817	Sliding-clamp-loader large subunit, C-terminal domain	Domain
A [auth B], B [auth C], C [auth D], D [auth E]	IPR003593	AAA+ ATPase domain	Domain
A [auth B], B [auth C], C [auth D], D [auth E]	IPR003959	ATPase, AAA-type, core	Domain
A [auth B], B [auth C], C [auth D], D [auth E]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
E [auth A]	IPR031868	Sliding-clamp-loader small subunit gp62	Family
F [auth G], G [auth H], H [auth F]	IPR046938	DNA clamp superfamily	Homologous Superfamily
F [auth G], G [auth H], H [auth F]	IPR046389	Sliding clamp	Family
F [auth G], G [auth H], H [auth F]	IPR004190	DNA polymerase processivity factor	Domain
F [auth G], G [auth H], H [auth F]	IPR015200	Sliding clamp, C-terminal	Domain

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.