1IZ6 | pdb_00001iz6

Crystal Structure of Translation Initiation Factor 5A from Pyrococcus Horikoshii

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)
C	d1iz6c1	All beta proteins	SH3-like barrel	Translation proteins SH3-like domain	eIF5a N-terminal domain-like	Eukaryotic initiation translation factor 5a (eIF5a)	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
C	d1iz6c2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a)	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
B	d1iz6b1	All beta proteins	SH3-like barrel	Translation proteins SH3-like domain	eIF5a N-terminal domain-like	Eukaryotic initiation translation factor 5a (eIF5a)	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
B	d1iz6b2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a)	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
A	d1iz6a1	All beta proteins	SH3-like barrel	Translation proteins SH3-like domain	eIF5a N-terminal domain-like	Eukaryotic initiation translation factor 5a (eIF5a)	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
A	d1iz6a2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a)	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Nucleic acid-binding proteins	8042623	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Translation proteins SH3-like KOW motif containing domain	8042622	3000334	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Translation proteins SH3-like KOW motif containing domain	8042622	3000334	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8042623	3000135	SCOP2B (2022-06-29)
A	SCOP2 Family	eIF5a N-terminal domain-like	8030243	4001758	SCOP2 (2022-06-29)
A	SCOP2 Family	Cold shock DNA-binding domain-like	8030244	4001909	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Translation proteins SH3-like KOW motif containing domain	8042622	3000334	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8042623	3000135	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)
C	Stap_Strp_toxin	e1iz6C1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (develop294)
C	Chromo	e1iz6C2	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Chromo	ECOD (develop294)
B	Stap_Strp_toxin	e1iz6B1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (develop294)
B	Chromo	e1iz6B2	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Chromo	ECOD (develop294)
A	IF5A-like_N	e1iz6A2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IF5A-like_N	ECOD (develop294)
A	Stap_Strp_toxin	e1iz6A1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.30.30.30	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	2.30.30.30	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	2.30.30.30	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Initiation Factor 5A	translation factor activity translation initiation factor activity translation elongation factor activity ribonucleoprotein complex binding protein-containing complex binding binding ribosome binding RNA binding nucleic acid binding	regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process regulation of translational elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process regulation of translational elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression positive regulation of translational elongation biosynthetic process positive regulation of gene expression regulation of translation translational elongation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of cellular component organization positive regulation of cellular component organization protein-containing complex disassembly regulation of protein-containing complex disassembly cellular component organization translational termination cellular component organization or biogenesis positive regulation of protein-containing complex disassembly cellular component disassembly protein-containing complex organization regulation of translational termination positive regulation of translational termination	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
A, B, C	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
A, B, C	IPR001884	Translation elongation factor IF5A-like	Family
A, B, C	IPR048670	Translation initiation factor 5A-like, N-terminal	Domain
A, B, C	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B, C	IPR019769	Translation initiation factor 5A, hypusine site	PTM
A, B, C	IPR022847	Translation elongation factor IF5A, archaeal	Family
A, B, C	IPR020189	Translation initiation factor 5A, C-terminal	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.