1KK1

Structure of the large gamma subunit of initiation factor eIF2 from Pyrococcus abyssi-G235D mutant complexed with GDPNP-Mg2+

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)
A	d1kk1a1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Elongation factors	Initiation factor eIF2 gamma subunit, domain II	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
A	d1kk1a2	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	Initiation factor eIF2 gamma subunit	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
A	d1kk1a3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Initiation factor eIF2 gamma subunit, N-terminal (G) domain	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8019773	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8019789	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8019773	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8019777	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nop10-like SnoRNP Znf-like	8093412	3000486	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	GTP_EFTU_D2_1	e1kk1A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
A	eIF2_C	e1kk1A2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: eIF2_C	ECOD (1.6)
A	MnmE_helical_2nd	e1kk1A4	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	PRK13130	e1kk1A3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PRK13130	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	PF09173	Initiation factor eIF2 gamma, C terminal (eIF2_C)	Initiation factor eIF2 gamma, C terminal	Members of this family, which are found in the initiation factors eIF2 and EF-Tu, adopt a structure consisting of a beta barrel with Greek key topology. They are required for formation of the ternary complex with GTP and initiator tRNA [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	eIF2gamma	translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding nucleic acid binding translation initiation factor activity translation factor activity, RNA binding translation elongation factor activity RNA binding tRNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding nucleic acid binding translation initiation factor activity translation factor activity, RNA binding translation elongation factor activity RNA binding tRNA 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 metal ion 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	ribonucleoprotein complex biogenesis protein-containing complex organization primary metabolic process translation gene expression macromolecule biosynthetic process protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly biosynthetic process protein-containing complex assembly cytoplasmic translation ribonucleoprotein complex biogenesis protein-containing complex organization primary metabolic process translation gene expression macromolecule biosynthetic process protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly biosynthetic process protein-containing complex assembly cytoplasmic translation cellular process cytoplasmic translational initiation metabolic process translational initiation cellular component organization or biogenesis protein metabolic process macromolecule metabolic process formation of translation preinitiation complex	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR005225	Small GTP-binding domain	Domain
A	IPR022424	Translation initiation factor 2, gamma subunit	Family
A	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
A	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A	IPR050543	Eukaryotic Initiation Factor 2 Gamma Subunit	Family
A	IPR044128	Initiation factor eIF2 gamma, GTP-binding domain	Domain
A	IPR015256	Initiation factor eIF2 gamma, C-terminal	Domain
A	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A	IPR044127	Initiation factor eIF2 gamma, domain 2	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.