2PJP | pdb_00002pjp

Structure of the mRNA-binding domain of elongation factor SelB from E.coli in complex with SECIS RNA

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2 Family	SelB C-terminal region	8058130	4000324	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Winged helix DNA-binding domain	8058132	3000034	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Winged helix DNA-binding domain	8058131	3000034	SCOP2 (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 [auth A]	HTH_3	e2pjpA1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: HTH_3	ECOD (v294.1)
B [auth A]	Gal-bind_lectin	e2pjpA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gal-bind_lectin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF09107	Elongation factor SelB, winged helix (WHD_3rd_SelB)	Elongation factor SelB, winged helix	Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DN ...	Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DNA and RNA binding [1].	Domain
B [auth A]	PF21214	Selenocysteine-specific elongation factor, winged helix domain (WHD_2nd_SelB_bact)	Selenocysteine-specific elongation factor, winged helix domain	This domain is found in Selenocysteine-specific elongation factor from Escherichia coli (SelB) and similar bacterial sequences. SelB is a translation factor necessary for the incorporation of selenocysteine into proteins. The C-terminal region of thi ...	This domain is found in Selenocysteine-specific elongation factor from Escherichia coli (SelB) and similar bacterial sequences. SelB is a translation factor necessary for the incorporation of selenocysteine into proteins. The C-terminal region of this protein in bacteria shows four winged-helix (WH) domains arranged in tandem, which form two globular structures. This entry represents the second pair of WH domains (WH3 and 4). Each WH domain is an alpha-beta structure consisting of three alpha-helices and a twisted three- stranded antiparallel beta-sheet [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A]	Selenocysteine-specific elongation factor	guanyl nucleotide binding binding nucleotide binding GDP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding guanyl nucleotide binding binding nucleotide binding GDP binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding translation factor activity translation elongation factor activity selenocysteine insertion sequence binding RNA binding nucleic acid binding mRNA binding tRNA binding GTP binding purine ribonucleoside triphosphate 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 metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process alpha-amino acid metabolic process selenocysteine incorporation regulation of cellular process protein biosynthetic process regulation of primary metabolic process selenocysteine metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process alpha-amino acid metabolic process 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 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 macromolecule metabolic process regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
A [auth B]	SECIS RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR015190	Translation elongation factor SelB, winged helix, type 2	Domain
B [auth A]	IPR000795	Translational (tr)-type GTP-binding domain	Domain
B [auth A]	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
B [auth A]	IPR057335	Selenocysteine-specific elongation factor, beta-barrel domain	Domain
B [auth A]	IPR031157	Tr-type G domain, conserved site	Conserved Site
B [auth A]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B [auth A]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B [auth A]	IPR048931	Selenocysteine-specific elongation factor, second winged helix domain	Domain
B [auth A]	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
B [auth A]	IPR050543	Eukaryotic Initiation Factor 2 Gamma Subunit	Family
B [auth A]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
B [auth A]	IPR015191	Elongation factor SelB, fourth winged-helix domain	Domain
B [auth A]	IPR004535	Translation elongation factor, selenocysteine-specific	Family
B [auth A]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth A]	IPR048649	Selenocysteine-specific elongation factor, first winged helix domain	Domain

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.