2YHT

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)
B	d2yhtb_	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)
E	d2yhte_	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)
G	d2yhtg_	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)
K	d2yhtk_	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)
C	d2yhtc_	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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
G	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)
K	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8044520	3000419	SCOP2B (2022-06-29)
L	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)
B	LSM	e2yhtB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
D	LSM	e2yhtD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E	LSM	e2yhtE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F	LSM	e2yhtF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
G	LSM	e2yhtG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
H	LSM	e2yhtH1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
I	LSM	e2yhtI1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
J	LSM	e2yhtJ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
K	LSM	e2yhtK1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
A	LSM	e2yhtA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
C	LSM	e2yhtC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
L	LSM	e2yhtL1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	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)
E	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)
G	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)
K	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)
C	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)

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 organic cyclic compound binding nucleic acid binding RNA binding RNA folding chaperone	regulation of cellular process catabolic process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of biological quality regulation of nucleobase-containing compound metabolic process RNA catabolic process regulation of cellular process catabolic process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of biological quality regulation of nucleobase-containing compound metabolic process RNA catabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process 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 organic substance catabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription 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 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 organonitrogen compound metabolic process regulation of protein metabolic process translation positive regulation of translation, ncRNA-mediated positive regulation of gene expression regulation of translation positive regulation of cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic 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 negative regulation of cellular biosynthetic process 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 anatomical structure cytoplasm cellular anatomical entity 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 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.