3MMP

Structure of the Qb replicase, an RNA-dependent RNA polymerase consisting of viral and host proteins

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)
A	SCOP2B Superfamily	Elongation factor Ts (EF-Ts) dimerisation domain	8035038	3000908	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8056531	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8056533	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	UBA-like	8032443	3001235	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Elongation factor Ts (EF-Ts) dimerisation domain	8032444	3000908	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8056530	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-Tu post-G domain-like	8056531	3002024	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Elongation factor Ts (EF-Ts) dimerisation domain	8032444	3000908	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Elongation factor Ts (EF-Ts) dimerisation domain	8035038	3000908	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-Tu post-G domain-like	8056533	3002024	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8056530	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	UBA-like	8032443	3001235	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	PF03144	e3mmpA7	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PF03144	ECOD (1.6)
A	PF03143	e3mmpA6	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: PF03143	ECOD (1.6)
A	F_UNCLASSIFIED	e3mmpA5	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF00889	e3mmpA2	A: a+b two layers	X: T-fold	H: Elongation factor Ts (EF-Ts), dimerisation domain (From Topology)	T: Elongation factor Ts (EF-Ts), dimerisation domain	F: PF00889	ECOD (1.6)
A	PF00009	e3mmpA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00009	ECOD (1.6)
C	PF03144	e3mmpC5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PF03144	ECOD (1.6)
C	PF03143	e3mmpC4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: PF03143	ECOD (1.6)
C	F_UNCLASSIFIED	e3mmpC11	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF00889	e3mmpC7	A: a+b two layers	X: T-fold	H: Elongation factor Ts (EF-Ts), dimerisation domain (From Topology)	T: Elongation factor Ts (EF-Ts), dimerisation domain	F: PF00889	ECOD (1.6)
C	PF00009	e3mmpC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00009	ECOD (1.6)
B [auth G]	PF03431	e3mmpG2	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: PF03431	ECOD (1.6)
B [auth G]	PF03431	e3mmpG1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: PF03431	ECOD (1.6)
D [auth F]	PF03431	e3mmpF2	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: PF03431	ECOD (1.6)
D [auth F]	PF03431	e3mmpF1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: PF03431	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00889	Elongation factor TS (EF_TS)	Elongation factor TS	-	Family
A, C	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
A, C	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
A, C	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
B [auth G], D [auth F]	PF03431	RNA replicase, beta-chain (RNA_replicase_B)	RNA replicase, beta-chain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Elongation factor Tu 2, Elongation factor Ts	translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding translation factor activity, RNA binding 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 translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding translation factor activity, RNA binding 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 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 RNA 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	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process translational elongation organic substance biosynthetic process metabolic process cellular process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process translational elongation organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process response to stimulus response to chemical response to antibiotic	membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol protein-containing complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex cell periphery plasma membrane
B [auth G], D [auth F]	RNA-directed RNA polymerase beta chain	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding binding organic cyclic compound binding nucleic acid binding nucleoside phosphate binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding binding organic cyclic compound binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	cellular biosynthetic process cellular 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral genome replication biosynthetic process cellular biosynthetic process cellular 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral genome replication biosynthetic process viral RNA genome replication organic cyclic compound biosynthetic process viral process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR014039	Translation elongation factor EFTs/EF1B, dimerisation	Domain
A, C	IPR018101	Translation elongation factor Ts, conserved site	Conserved Site
A, C	IPR001816	Translation elongation factor EFTs/EF1B	Family
A, C	IPR036402	Elongation factor Ts, dimerisation domain superfamily	Homologous Superfamily
A, C	IPR009060	UBA-like superfamily	Homologous Superfamily
A, C	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A, C	IPR033720	Elongation factor Tu, domain 2	Domain
A, C	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
A, C	IPR031157	Tr-type G domain, conserved site	Conserved Site
A, C	IPR004541	Translation elongation factor EFTu/EF1A, bacterial/organelle	Family
A, C	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A, C	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, C	IPR004160	Translation elongation factor EFTu/EF1A, C-terminal	Domain
A, C	IPR005225	Small GTP-binding protein domain	Domain
A, C	IPR041709	Elongation factor Tu (EF-Tu), GTP-binding domain	Domain
A, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth G], D [auth F]	IPR007096	RNA-directed RNA polymerase, catalytic domain, bacteriophage	Domain
B [auth G], D [auth F]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
B [auth G], D [auth F]	IPR005093	RNA-directed RNA polymerase beta-chain	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 R01GM133198.