2YHT | pdb_00002yht

Crystal structure of Hfq riboregulator from E. coli (P1 space group)

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)
C	d2yhtc_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2yhtd_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2yhtf_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d2yhth_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d2yhti_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d2yhtj_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L	d2yhtl_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K	d2yhtk_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d2yhtg_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2yhte_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2yhtb_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2yhta_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	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)
C	Reo_sigma1	e2yhtC1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
D	Reo_sigma1	e2yhtD1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
F	Reo_sigma1	e2yhtF1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
H	Reo_sigma1	e2yhtH1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
I	Reo_sigma1	e2yhtI1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
J	Reo_sigma1	e2yhtJ1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
L	Reo_sigma1	e2yhtL1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
K	Reo_sigma1	e2yhtK1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
G	Reo_sigma1	e2yhtG1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
E	Reo_sigma1	e2yhtE1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
B	Reo_sigma1	e2yhtB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
A	Reo_sigma1	e2yhtA1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
F	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
H	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
I	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
J	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
L	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
K	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
G	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
E	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF17209	Hfq protein (Hfq)	Hfq protein		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PROTEIN HFQ	DNA binding bent DNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding DNA binding bent DNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding RNA binding tRNA binding RNA folding chaperone	regulation of cellular process catabolic process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of biological quality regulation of nucleobase-containing compound metabolic process RNA catabolic process regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular process catabolic process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of biological quality regulation of nucleobase-containing compound metabolic process RNA catabolic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression biosynthetic process regulation of RNA stability nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of translation, ncRNA-mediated positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process translation positive regulation of translation, ncRNA-mediated positive regulation of gene expression regulation of translation tRNA metabolic process tRNA processing RNA processing negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process sRNA-mediated post-transcriptional gene silencing negative regulation of metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing	intracellular organelle bacterial nucleoid cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle nucleoid cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR005001	RNA-binding protein Hfq	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR047575	Sm domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR010920	LSM domain superfamily	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.