2CZJ | pdb_00002czj

Crystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8

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	d2czja1	All beta proteins	Small protein B (SmpB)	Small protein B (SmpB)	Small protein B (SmpB)	Small protein B (SmpB)	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B [auth C]	d2czjc1	All beta proteins	Small protein B (SmpB)	Small protein B (SmpB)	Small protein B (SmpB)	Small protein B (SmpB)	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
D [auth G]	d2czjg1	All beta proteins	Small protein B (SmpB)	Small protein B (SmpB)	Small protein B (SmpB)	Small protein B (SmpB)	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C [auth E]	d2czje1	All beta proteins	Small protein B (SmpB)	Small protein B (SmpB)	Small protein B (SmpB)	Small protein B (SmpB)	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Small protein B (SmpB)	8042603	3000956	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Small protein B (SmpB)	8042603	3000956	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	Small protein B (SmpB)	8042603	3000956	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Small protein B (SmpB)	8042603	3000956	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	CSD	e2czjA1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: CSD	ECOD (v294.1)
B [auth C]	CSD	e2czjC1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: CSD	ECOD (v294.1)
D [auth G]	CSD	e2czjG1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: CSD	ECOD (v294.1)
C [auth E]	CSD	e2czjE1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: CSD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.280.10	Mainly Beta	Beta Barrel	Small Protein B	Chain: A	CATH (4.3.0)
B [auth C]	2.40.280.10	Mainly Beta	Beta Barrel	Small Protein B	Chain: A	CATH (4.3.0)
D [auth G]	2.40.280.10	Mainly Beta	Beta Barrel	Small Protein B	Chain: A	CATH (4.3.0)
C [auth E]	2.40.280.10	Mainly Beta	Beta Barrel	Small Protein B	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth E], D [auth G]	PF01668	SmpB protein (SmpB)	SmpB protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth B], F [auth D], G [auth F], H	tmRNA (63-MER)	-	-	-
A, B [auth C], C [auth E], D [auth G]	SsrA-binding protein	RNA binding binding rRNA binding nucleic acid binding	primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process biosynthetic process trans-translation translational elongation metabolic process cellular process macromolecule metabolic process protein metabolic process cellular component disassembly trans-translation-dependent protein tagging primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process biosynthetic process trans-translation translational elongation metabolic process cellular process macromolecule metabolic process protein metabolic process cellular component disassembly trans-translation-dependent protein tagging ribosome disassembly cellular component organization organelle organization organelle disassembly cytoplasmic translation cytoplasmic translational elongation cellular component organization or biogenesis rescue of stalled cytosolic ribosome	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth E], D [auth G]	IPR020081	SsrA-binding protein, conserved site	Conserved Site
A, B [auth C], C [auth E], D [auth G]	IPR023620	Small protein B	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G]	IPR000037	SsrA-binding protein	Family

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.