4ACA | pdb_00004aca

CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR SELB FROM METHANOCOCCUS MARIPALUDIS, APO FORM

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d4acad1	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	d4acad3	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	d4acad4	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	d4acac1	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	d4acac3	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	d4acac4	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	d4acac5	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Methanococcus maripaludis ) [TaxId: 39152 ],	SCOPe (2.08)
B	d4acab1	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	d4acab3	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	d4acab4	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	d4acaa1	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	d4acaa3	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	d4acaa4	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	d4acaa5	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
D	SCOP2B Superfamily	EF-Tu post-G domain-like	8091672	3002024	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EF-Tu post-G domain-like	8043377	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)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8043379	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-Tu post-G domain-like	8043377	3002024	SCOP2B (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)
B	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	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)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8043379	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8043376	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8043377	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8091672	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)
D	selB_2nd_1	e4acaD4	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	e4acaD8	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	e4acaD2	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	e4acaD10	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	e4acaC4	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	e4acaC8	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	e4acaC2	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	e4acaC10	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	e4acaB4	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	e4acaB12	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	e4acaB2	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	e4acaB14	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	selB_2nd_1	e4acaA4	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	e4acaA9	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	e4acaA2	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	e4acaA1	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)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.2.0)
D	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.2.0)
D	2.40.10.190	Mainly Beta	Beta Barrel	Thrombin, subunit H	translation elongation factor selb, chain A, domain 4	CATH (4.2.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.2.0)
C	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.2.0)
C	2.40.10.190	Mainly Beta	Beta Barrel	Thrombin, subunit H	translation elongation factor selb, chain A, domain 4	CATH (4.2.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.2.0)
B	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.2.0)
B	2.40.10.190	Mainly Beta	Beta Barrel	Thrombin, subunit H	translation elongation factor selb, chain A, domain 4	CATH (4.2.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.2.0)
A	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.2.0)
A	2.40.10.190	Mainly Beta	Beta Barrel	Thrombin, subunit H	translation elongation factor selb, chain A, domain 4	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	TRANSLATION ELONGATION FACTOR SELB	translation factor activity translation elongation factor activity RNA binding binding nucleic acid 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 translation factor activity translation elongation factor activity RNA binding binding nucleic acid 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 protein biosynthetic 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 selenocysteine incorporation regulation of cellular process protein biosynthetic 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.