2OM7 | pdb_00002om7

Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors

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)
K [auth E]	d2om7e1	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Ribosome complexes	70S ribosome functional complex	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
L [auth K]	d2om7k1	Multi-domain proteins (alpha and beta)	Ribosomal protein L1	Ribosomal protein L1	Ribosomal protein L1	Ribosomal protein L1	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
N	d2om7n1	Alpha and beta proteins (a/b)	Flavodoxin-like	Ribosomal protein S2	Ribosomal protein S2	Ribosomal protein S2	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K [auth E]	SCOP2B Superfamily	Nucleic acid-binding proteins	8044021	3000135	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	SIS domain/Ribosomal protein S2-like	8044010	3001397	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)
K [auth E]	Ribosom_S12_S23	e2om7E1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Ribosom_S12_S23	ECOD (1.6)
L [auth K]	Ribosomal_L1_2nd_1	e2om7K6	A: a+b two layers	X: a+b domain in Ribosomal protein L1 (From Topology)	H: a+b domain in Ribosomal protein L1 (From Topology)	T: a+b domain in Ribosomal protein L1	F: Ribosomal_L1_2nd_1	ECOD (1.6)
L [auth K]	Ribosomal_L1_1st	e2om7K5	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Rossmann-like domain in Ribosomal protein L1 (From Topology)	T: Rossmann-like domain in Ribosomal protein L1	F: Ribosomal_L1_1st	ECOD (1.6)
M [auth L]	GTP_EFTU_D2	e2om7L21	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2	ECOD (1.6)
M [auth L]	EFG_IV	e2om7L24	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)
M [auth L]	EFG_C	e2om7L20	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)
M [auth L]	EFG_II	e2om7L22	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)
M [auth L]	MnmE_helical_2nd	e2om7L23	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)
N	Ribosomal_S2	e2om7N1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Ribosomal protein S2/SIS domain (From Topology)	T: Ribosomal protein S2/SIS domain	F: Ribosomal_S2	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
K [auth E]	PF00164	Ribosomal protein S12/S23 (Ribosom_S12_S23)	Ribosomal protein S12/S23	This protein is known as S12 in bacteria and archaea and S23 in eukaryotes.	Domain
M [auth L]	PF00679	Elongation factor G C-terminus (EFG_C)	Elongation factor G C-terminus	This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.	Domain
M [auth L]	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
M [auth L]	PF14492	Elongation Factor G, domain III (EFG_III)	Elongation Factor G, domain III	This domain is found in Elongation Factor G. It shares a similar structure with domain V (Pfam:PF00679). Structural studies in drosophila indicate this is domain 3 [1].	Domain
M [auth L]	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
M [auth L]	PF03764	Elongation factor G, domain IV (EFG_IV)	Elongation factor G, domain IV	This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold.	Domain
N	PF00318	Ribosomal protein S2 (Ribosomal_S2)	Ribosomal protein S2	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Fragment of 16S rRNA (h14)	-	-	-
J [auth M]	p/E-tRNA	-	-	-
K [auth E]	30S ribosomal protein S12	RNA binding binding tRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome rRNA binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome
L [auth K]	50S ribosomal protein L1	RNA binding binding tRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome rRNA binding	regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process regulation of metabolic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome large ribosomal subunit
M [auth L]	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 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	cellular component organization cellular component disassembly organelle organization organelle disassembly ribosome disassembly cellular process cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm
N	30S ribosomal protein S2	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process	cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol
B	Fragment of 16S rRNA (h15)	-	-	-
C	Fragment of 16S rRNA (h44)	-	-	-
D	16S ribosomal RNA (H5)	-	-	-
E [auth F]	Fragment of23S rRNA (H95)	-	-	-
F [auth G]	Fragment of23S rRNA (H68)	-	-	-
G [auth H]	Fragment of23S rRNA (H89)	-	-	-
H [auth I]	Fragment of23S rRNA (H42-44)	-	-	-
I [auth J]	Fragment of23S rRNA (H76)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
K [auth E]	IPR006032	Small ribosomal subunit protein uS12	Family
K [auth E]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
K [auth E]	IPR005679	Ribosomal protein uS12, bacterial-type	Family
L [auth K]	IPR023673	Large ribosomal subunit protein uL1, conserved site	Conserved Site
L [auth K]	IPR016095	Large ribosomal subunit protein uL1, 3-layer alpha/beta-sandwich domain	Homologous Superfamily
L [auth K]	IPR005878	Large ribosomal subunit protein uL1, bacterial-type	Family
L [auth K]	IPR023674	Ribosomal protein uL1-like	Homologous Superfamily
L [auth K]	IPR002143	Large ribosomal subunit protein uL1	Family
L [auth K]	IPR028364	Ribosomal protein uL1/ribosomal biogenesis protein	Family
M [auth L]	IPR005225	Small GTP-binding domain	Domain
M [auth L]	IPR005517	Translation elongation factor EFG/EF2, domain IV	Domain
M [auth L]	IPR004540	Translation elongation factor EFG/EF2	Family
M [auth L]	IPR000795	Translational (tr)-type GTP-binding domain	Domain
M [auth L]	IPR000640	Elongation factor EFG, domain V-like	Domain
M [auth L]	IPR031157	Tr-type G domain, conserved site	Conserved Site
M [auth L]	IPR009022	Elongation factor G, domain III	Domain
M [auth L]	IPR035647	EF-G domain III/V-like	Homologous Superfamily
M [auth L]	IPR041095	Elongation Factor G, domain II	Domain
M [auth L]	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
M [auth L]	IPR047872	Elongation factor G, domain IV	Domain
M [auth L]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
M [auth L]	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
M [auth L]	IPR035649	EFG, domain V	Domain
M [auth L]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
M [auth L]	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
N	IPR005706	Small ribosomal subunit protein uS2, bacteria/mitochondria/plastid	Family
N	IPR023591	Small ribosomal subunit protein uS2, flavodoxin-like domain superfamily	Homologous Superfamily
N	IPR018130	Small ribosomal subunit protein uS2, conserved site	Conserved Site
N	IPR001865	Small ribosomal subunit protein uS2	Family