4AC9

CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR SELB FROM METHANOCOCCUS MARIPALUDIS IN COMPLEX WITH GDP

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	d4ac9a1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Elongation factors	Elongation factor SelB, domains 2 and 4	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
A	d4ac9a3	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 SelB, domain 3	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
A	d4ac9a4	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Elongation factor SelB, N-terminal domain	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
A	d4ac9a5	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
C	d4ac9c1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Elongation factors	Elongation factor SelB, domains 2 and 4	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
C	d4ac9c3	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 SelB, domain 3	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
C	d4ac9c4	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Elongation factor SelB, N-terminal domain	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
C	d4ac9c5	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
D	d4ac9d1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Elongation factors	Elongation factor SelB, domains 2 and 4	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
D	d4ac9d3	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 SelB, domain 3	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
D	d4ac9d4	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Elongation factor SelB, N-terminal domain	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
B	d4ac9b1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Elongation factors	Elongation factor SelB, domains 2 and 4	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
B	d4ac9b3	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 SelB, domain 3	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
B	d4ac9b4	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Elongation factor SelB, N-terminal domain	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	IF2 C-terminal domain-like	8030998	4004052	SCOP2 (2022-06-29)
A	SCOP2 Family	EF-Tu C-terminal domain-like	8031000	4002110	SCOP2 (2022-06-29)
A	SCOP2 Family	Translation factor common region-like	8031001	4004050	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	EF-Tu post-G domain-like	8043377	3002024	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	EF-Tu post-G domain-like	8091672	3002024	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ras-like P-loop GTPases	8043379	3002022	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	EF-Tu post-G domain-like	8043376	3002024	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	EF-Tu post-G domain-like	8043376	3002024	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-Tu post-G domain-like	8091672	3002024	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-Tu post-G domain-like	8043377	3002024	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8043379	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EF-Tu post-G domain-like	8091672	3002024	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8043379	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EF-Tu post-G domain-like	8043376	3002024	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EF-Tu post-G domain-like	8043377	3002024	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-Tu post-G domain-like	8091672	3002024	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-Tu post-G domain-like	8043377	3002024	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8043379	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-Tu post-G domain-like	8043376	3002024	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	selB_2nd_1	e4ac9A4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: selB_2nd_1	ECOD (1.6)
A	GTP_EFTU_D2_1	e4ac9A9	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
A	eSelB_III_1	e4ac9A2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: eSelB_III_1	ECOD (1.6)
A	MnmE_helical_2nd	e4ac9A1	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)
C	selB_2nd_1	e4ac9C4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: selB_2nd_1	ECOD (1.6)
C	GTP_EFTU_D2_1	e4ac9C2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
C	eSelB_III_1	e4ac9C3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: eSelB_III_1	ECOD (1.6)
C	MnmE_helical_2nd	e4ac9C1	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)
D	selB_2nd_1	e4ac9D4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: selB_2nd_1	ECOD (1.6)
D	GTP_EFTU_D2_1	e4ac9D11	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
D	eSelB_III_1	e4ac9D2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: eSelB_III_1	ECOD (1.6)
D	MnmE_helical_2nd	e4ac9D13	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)
B	selB_2nd_1	e4ac9B4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: selB_2nd_1	ECOD (1.6)
B	GTP_EFTU_D2_1	e4ac9B8	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
B	eSelB_III_1	e4ac9B2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: eSelB_III_1	ECOD (1.6)
B	MnmE_helical_2nd	e4ac9B10	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)

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)
A	2.40.10.190	Mainly Beta	Beta Barrel	Thrombin, subunit H	translation elongation factor selb, chain A, domain 4	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)
C	2.40.10.190	Mainly Beta	Beta Barrel	Thrombin, subunit H	translation elongation factor selb, chain A, domain 4	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
D	2.40.10.190	Mainly Beta	Beta Barrel	Thrombin, subunit H	translation elongation factor selb, chain A, domain 4	CATH (4.3.0)
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)
B	2.40.10.190	Mainly Beta	Beta Barrel	Thrombin, subunit H	translation elongation factor selb, chain A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, B, C, D	PF21440	Archaeal selenocysteine-specific elongation factor, domain III (aSelB_III)	Archaeal selenocysteine-specific elongation factor, domain III	Selenocysteine-specific elongation factor (SelB) is a transcription factor necessary for the incorporation of selenocysteine into proteins. This entry represents domain III of archaeal SelB, which adopts a beta-barrel fold and is homologous to domain ...	Selenocysteine-specific elongation factor (SelB) is a transcription factor necessary for the incorporation of selenocysteine into proteins. This entry represents domain III of archaeal SelB, which adopts a beta-barrel fold and is homologous to domain III of EF-Tu [1].	Domain
A, B, C, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	MJ0495-LIKE PROTEIN	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 RNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate 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 RNA 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	selenocysteine incorporation regulation of cellular process regulation of primary metabolic process post-transcriptional regulation of gene expression protein metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process translational readthrough gene expression translation selenocysteine incorporation regulation of cellular process regulation of primary metabolic process post-transcriptional regulation of gene expression protein metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process translational readthrough gene expression translation macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of translation translational elongation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR005225	Small GTP-binding domain	Domain
A, B, C, D	IPR038661	Large ribosomal subunit protein eL33 superfamily	Homologous Superfamily
A, B, C, D	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A, B, C, D	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
A, B, C, D	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A, B, C, D	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, B, C, D	IPR050055	Elongation factor Tu GTPase	Family
A, B, C, D	IPR004535	Translation elongation factor, selenocysteine-specific	Family
A, B, C, D	IPR048956	Selenocysteine-specific elongation factor, domain III, archaea	Domain
A, B, C, D	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.