1JQM | pdb_00001jqm

Fitting of L11 protein and elongation factor G (EF-G) in the cryo-em map of e. coli 70S ribosome bound with EF-G, GDP and fusidic acid

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d1jqmb_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Ribosome complexes	70S ribosome functional complex	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1jqma_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Ribosome complexes	70S ribosome functional complex	(Escherichia coli ) [TaxId: 562 ],	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-G C-terminal domain-like	8038318	3001287	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-Tu post-G domain-like	8038315	3002024	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8038317	3000100	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8038316	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-G C-terminal domain-like	8038320	3001287	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosomal protein L11, C-terminal domain	8036651	3001186	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosomal L11/L12e N-terminal domain-like	8035082	3000950	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)
B	GTP_EFTU_D2	e1jqmB2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2	ECOD (1.6)
B	EFG_IV	e1jqmB3	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: EFG_IV	ECOD (1.6)
B	EFG_C	e1jqmB4	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: EFG_C	ECOD (1.6)
B	EFG_II	e1jqmB5	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: EFG_II	ECOD (1.6)
B	MnmE_helical_2nd	e1jqmB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
A	Ribosomal_L11	e1jqmA1	A: alpha arrays	X: HTH	H: HTH	T: Ribosomal protein L11, C-terminal domain	F: Ribosomal_L11	ECOD (1.6)
A	Ribosomal_L11_N	e1jqmA2	A: a+b two layers	X: Ribosomal protein L11/L12e N-terminal domain-like	H: Ribosomal protein L11/L12e N-terminal domain (From Topology)	T: Ribosomal protein L11/L12e N-terminal domain	F: Ribosomal_L11_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03946	Ribosomal protein L11, N-terminal domain (Ribosomal_L11_N)	Ribosomal protein L11, N-terminal domain	The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain.	Domain
A	PF00298	Ribosomal protein L11, RNA binding domain (Ribosomal_L11)	Ribosomal protein L11, RNA binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Elongation Factor G	translation factor activity translation elongation factor activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding translation factor activity translation elongation factor activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding magnesium ion binding metal ion binding GDP binding ribonucleoprotein complex binding protein-containing complex binding ribosome 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	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 component organization cellular component disassembly organelle organization 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 component organization cellular component disassembly organelle organization organelle disassembly ribosome disassembly cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm
A	50S Ribosomal protein L11	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding large ribosomal subunit rRNA binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol large ribosomal subunit

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR005517	Translation elongation factor EFG/EF2, domain IV	Domain
B	IPR000795	Translational (tr)-type GTP-binding domain	Domain
B	IPR035647	EF-G domain III/V-like	Homologous Superfamily
B	IPR041095	Elongation Factor G, domain II	Domain
B	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
B	IPR047872	Elongation factor G, domain IV	Domain
B	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
B	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
B	IPR035649	EFG, domain V	Domain
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
B	IPR005225	Small GTP-binding domain	Domain
B	IPR004540	Translation elongation factor EFG/EF2	Family
B	IPR000640	Elongation factor EFG, domain V-like	Domain
B	IPR031157	Tr-type G domain, conserved site	Conserved Site
B	IPR009022	Elongation factor G, domain III	Domain
A	IPR020785	Large ribosomal subunit protein uL11, conserved site	Conserved Site
A	IPR020783	Large ribosomal subunit protein uL11, C-terminal	Domain
A	IPR000911	Ribosomal protein uL11	Family
A	IPR036769	Large ribosomal subunit protein uL11, C-terminal domain superfamily	Homologous Superfamily
A	IPR020784	Large ribosomal subunit protein uL11, N-terminal	Domain
A	IPR036796	Large ribosomal subunit protein uL11, N-terminal domain superfamily	Homologous Superfamily
A	IPR006519	Large ribosomal subunit protein uL11, bacteria	Family