4Q7J | pdb_00004q7j

Complex structure of viral RNA polymerase

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4q7jb2	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Elongation factors	Elongation factor Tu (EF-Tu), domain 2	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4q7jb3	All beta proteins	Elongation factor/aminomethyltransferase common domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	Elongation factor Tu (EF-Tu)	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4q7jb1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Elongation factor Tu (EF-Tu), N-terminal (G) domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d4q7jf2	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Elongation factors	Elongation factor Tu (EF-Tu), domain 2	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d4q7jf3	All beta proteins	Elongation factor/aminomethyltransferase common domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	Elongation factor Tu (EF-Tu)	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d4q7jf1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Elongation factor Tu (EF-Tu), N-terminal (G) domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4q7ja1	All alpha proteins	RuvA C-terminal domain-like	UBA-like	TS-N domain	Elongation factor Ts (EF-Ts), N-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4q7ja3	Alpha and beta proteins (a+b)	EF-Ts domain-like	Elongation factor Ts (EF-Ts), dimerisation domain	Elongation factor Ts (EF-Ts), dimerisation domain	Elongation factor Ts (EF-Ts), dimerisation domain, C-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4q7ja2	Alpha and beta proteins (a+b)	EF-Ts domain-like	Elongation factor Ts (EF-Ts), dimerisation domain	Elongation factor Ts (EF-Ts), dimerisation domain	Elongation factor Ts (EF-Ts), dimerisation domain, N-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d4q7je1	All alpha proteins	RuvA C-terminal domain-like	UBA-like	TS-N domain	Elongation factor Ts (EF-Ts), N-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d4q7je3	Alpha and beta proteins (a+b)	EF-Ts domain-like	Elongation factor Ts (EF-Ts), dimerisation domain	Elongation factor Ts (EF-Ts), dimerisation domain	Elongation factor Ts (EF-Ts), dimerisation domain, C-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d4q7je2	Alpha and beta proteins (a+b)	EF-Ts domain-like	Elongation factor Ts (EF-Ts), dimerisation domain	Elongation factor Ts (EF-Ts), dimerisation domain	Elongation factor Ts (EF-Ts), dimerisation domain, N-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	EF-Tu post-G domain-like	8056350	3002024	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8056349	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-Tu post-G domain-like	8056352	3002024	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	EF-Tu post-G domain-like	8056350	3002024	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ras-like P-loop GTPases	8056349	3002022	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	EF-Tu post-G domain-like	8056352	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Elongation factor Ts (EF-Ts), dimerisation domain	8035038	3000908	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Elongation factor Ts (EF-Ts), dimerisation domain	8032444	3000908	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	UBA-like	8032443	3001235	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Elongation factor Ts (EF-Ts), dimerisation domain	8032444	3000908	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	UBA-like	8032443	3001235	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Elongation factor Ts (EF-Ts), dimerisation domain	8035038	3000908	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)
D	Pribosyltran	e4q7jD1	A: a/b three-layered sandwiches	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: Middle and GTPase effector domains in dynamin-related proteins	F: Pribosyltran	ECOD (v294.1)
H	Dynamin_M,GED	e4q7jH1	A: a/b three-layered sandwiches	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: Middle and GTPase effector domains in dynamin-related proteins	F: Dynamin_M,GED	ECOD (v294.1)
C	Pribosyltran	e4q7jC1	A: a/b three-layered sandwiches	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: Middle and GTPase effector domains in dynamin-related proteins	F: Pribosyltran	ECOD (v294.1)
G	Pribosyltran	e4q7jG1	A: a/b three-layered sandwiches	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: Middle and GTPase effector domains in dynamin-related proteins	F: Pribosyltran	ECOD (v294.1)
B	Pribosyltran	e4q7jB1	A: a/b three-layered sandwiches	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: Middle and GTPase effector domains in dynamin-related proteins	F: Pribosyltran	ECOD (v294.1)
F	Pribosyltran	e4q7jF1	A: a/b three-layered sandwiches	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: Middle and GTPase effector domains in dynamin-related proteins	F: Pribosyltran	ECOD (v294.1)
A	Pribosyltran	e4q7jA1	A: a/b three-layered sandwiches	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: Middle and GTPase effector domains in dynamin-related proteins	F: Pribosyltran	ECOD (v294.1)
E	Pribosyltran	e4q7jE1	A: a/b three-layered sandwiches	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: Middle and GTPase effector domains in dynamin-related proteins	F: Pribosyltran	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	3.30.479.20	Alpha Beta	2-Layer Sandwich	Tetrahydropterin Synthase	Chain A	CATH (4.3.0)
A	1.10.286.20	Mainly Alpha	Orthogonal Bundle	GTP Cyclohydrolase I	Chain A, domain 1	CATH (4.3.0)
E	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
E	3.30.479.20	Alpha Beta	2-Layer Sandwich	Tetrahydropterin Synthase	Chain A	CATH (4.3.0)
E	1.10.286.20	Mainly Alpha	Orthogonal Bundle	GTP Cyclohydrolase I	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, H	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain
B, F	PF00009	Elongation factor Tu GTP binding domain (GTP_EFTU)	Elongation factor Tu GTP binding domain	This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.	Domain
B, F	PF03143	Elongation factor Tu C-terminal domain (GTP_EFTU_D3)	Elongation factor Tu C-terminal domain	Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA [1] and binding to EF-Ts Pfam:PF00889 [2].	Domain
B, F	PF03144	Elongation factor Tu domain 2 (GTP_EFTU_D2)	Elongation factor Tu domain 2	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.	Domain
A, E	PF00889	Elongation factor TS (EF_TS)	Elongation factor TS	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, H	30S ribosomal protein S1	RNA binding binding nucleic acid binding mRNA binding single-stranded RNA binding structural molecule activity structural constituent of ribosome	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process translation gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of cytoplasmic translation negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process cytoplasmic translation metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of cytoplasmic translation regulation of metabolic process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of cytoplasmic translation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of gene expression ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribosome assembly	cellular anatomical structure membrane cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cellular anatomical structure membrane cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol
C, G	Q beta replicase	RNA-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 RNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding RNA-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 RNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process	-
B, F	Elongation factor Tu 1	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding guanosine tetraphosphate binding guanyl nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding purine nucleotide binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding guanosine tetraphosphate binding guanyl nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding translation factor activity translation elongation factor activity RNA binding nucleic acid binding GTP binding purine ribonucleoside triphosphate binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	response to stimulus response to chemical response to antibiotic primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process biosynthetic process translational elongation metabolic process cellular process macromolecule metabolic process protein metabolic process	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm protein-containing complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex
A, E	Elongation factor Ts	translation factor activity translation elongation factor activity GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process biosynthetic process translational elongation metabolic process cellular process macromolecule metabolic process protein metabolic process	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, H	IPR035104	Ribosomal protein S1-like	Family
D, H	IPR003029	S1 domain	Domain
D, H	IPR050437	Small ribosomal subunit protein bS1-like	Family
D, H	IPR000110	Small ribosomal subunit protein bS1	Family
D, H	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
C, G	IPR007096	RNA-directed RNA polymerase, catalytic domain, bacteriophage	Domain
C, G	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C, G	IPR005093	RNA-directed RNA polymerase beta-chain	Family
B, F	IPR005225	Small GTP-binding domain	Domain
B, F	IPR000795	Translational (tr)-type GTP-binding domain	Domain
B, F	IPR033720	Elongation factor Tu, domain 2	Domain
B, F	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
B, F	IPR031157	Tr-type G domain, conserved site	Conserved Site
B, F	IPR004541	Translation elongation factor EFTu/EF1A, bacterial/organelle	Family
B, F	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
B, F	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
B, F	IPR004160	Translation elongation factor EFTu/EF1A, C-terminal	Domain
B, F	IPR050055	Elongation factor Tu GTPase	Family
B, F	IPR041709	Elongation factor Tu (EF-Tu), GTP-binding domain	Domain
B, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, E	IPR014039	Translation elongation factor EFTs/EF1B, dimerisation	Domain
A, E	IPR018101	Translation elongation factor Ts, conserved site	Conserved Site
A, E	IPR001816	Translation elongation factor EFTs/EF1B	Family
A, E	IPR036402	Elongation factor Ts, dimerisation domain superfamily	Homologous Superfamily
A, E	IPR009060	UBA-like superfamily	Homologous Superfamily