1IZ6

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
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	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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Cold shock DNA-binding domain-like	8030244	4001909	SCOP2 (2022-06-29)
A	SCOP2 Family	eIF5a N-terminal domain-like	8030243	4001758	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8042623	3000135	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Translation proteins SH3-like KOW motif containing domain	8042622	3000334	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8042623	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Translation proteins SH3-like KOW motif containing domain	8042622	3000334	SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF01287	e1iz6A1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01287	ECOD (1.6)
A	PF21485	e1iz6A2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF21485	ECOD (1.6)
B	PF01287	e1iz6B1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01287	ECOD (1.6)
B	PF21485	e1iz6B2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF21485	ECOD (1.6)
C	PF01287	e1iz6C1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01287	ECOD (1.6)
C	PF21485	e1iz6C2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF21485	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF21485	Translation initiation factor 5A-like, N-terminal (IF5A-like_N)	Translation initiation factor 5A-like, N-terminal	This is the N-terminal domain of Translation initiation factor 5A from eukaryotes and archaea, which has a SH2-like fold. These proteins are involved in translation elongation and eIF5A is specifically required to promote peptide-bond formation betwe ...	This is the N-terminal domain of Translation initiation factor 5A from eukaryotes and archaea, which has a SH2-like fold. These proteins are involved in translation elongation and eIF5A is specifically required to promote peptide-bond formation between consecutive proline residues [1-5]. This entry also includes Woronin body major protein Hex1, which is similar to eIF5A.	Domain
A, B, C	PF01287	Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold (eIF-5a)	Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold	eIF5A, previously thought to be an initiation factor, has been shown to be required for peptide chain elongation in yeast [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Initiation Factor 5A	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 ribonucleoprotein complex binding protein-containing complex binding ribosome binding RNA binding	regulation of cellular process cellular biosynthetic process positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic 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 organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process regulation of cellular process cellular biosynthetic process positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic 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 organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular 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 positive regulation of cellular biosynthetic process protein-containing complex disassembly regulation of protein-containing complex disassembly translational termination cellular component disassembly regulation of translational termination positive regulation of translational termination regulation of cellular component organization positive regulation of cellular component organization cellular component organization cellular component organization or biogenesis positive regulation of protein-containing complex disassembly protein-containing complex organization	intracellular anatomical structure cytoplasm cellular anatomical entity

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	IPR020189	Translation elongation factor, IF5A C-terminal	Domain
A, B, C	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
A, B, C	IPR019769	Translation elongation factor, IF5A, hypusine site	PTM
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	IPR022847	Translation elongation factor IF5A, archaeal	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.