Annotations: 3SB2

Crystal Structure of the RNA chaperone Hfq from Herbaspirillum seropedicae SMR1

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)
F	d3sb2f_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Herbaspirillum seropedicae SmR1 ) [TaxId: 757424 ],	SCOPe (2.08)
E	d3sb2e_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Herbaspirillum seropedicae SmR1 ) [TaxId: 757424 ],	SCOPe (2.08)
D	d3sb2d_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Herbaspirillum seropedicae SmR1 ) [TaxId: 757424 ],	SCOPe (2.08)
C	d3sb2c_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Herbaspirillum seropedicae SmR1 ) [TaxId: 757424 ],	SCOPe (2.08)
B	d3sb2b_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Herbaspirillum seropedicae SmR1 ) [TaxId: 757424 ],	SCOPe (2.08)
A	d3sb2a_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	automated matches	(Herbaspirillum seropedicae SmR1 ) [TaxId: 757424 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058969	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058969	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058969	3000419	SCOP2B (2022-06-29)
C	SCOP2 Family	Pleiotropic translational regulator Hfq	8058968	4002164	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Sm-like ribonucleoproteins	8058969	3000419	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058969	3000419	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058969	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)
F	PUF	e3sb2F1	A: alpha arrays	X: Insertion subdomain in DsbA-like	H: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	T: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	F: PUF	ECOD (v295.2)
E	PUF	e3sb2E1	A: alpha arrays	X: Insertion subdomain in DsbA-like	H: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	T: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	F: PUF	ECOD (v295.2)
D	PUF	e3sb2D1	A: alpha arrays	X: Insertion subdomain in DsbA-like	H: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	T: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	F: PUF	ECOD (v295.2)
C	PUF	e3sb2C1	A: alpha arrays	X: Insertion subdomain in DsbA-like	H: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	T: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	F: PUF	ECOD (v295.2)
B	PUF	e3sb2B1	A: alpha arrays	X: Insertion subdomain in DsbA-like	H: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	T: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	F: PUF	ECOD (v295.2)
A	cNMP_binding	e3sb2A1	A: alpha arrays	X: Major vault protein (MVP) structural repeat domain	H: Major vault protein (MVP) structural repeat domain	T: Major vault protein (MVP) structural repeat domain	F: cNMP_binding	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	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)
D	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)
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	PF17209	Hfq protein (Hfq)	Hfq protein	This entry represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria [1]. It helps pair regulatory non-coding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA [2]. It ap ...	This entry represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria [1]. It helps pair regulatory non-coding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA [2]. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage [3]. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam:RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor [4]. The name Hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.	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	Protein hfq	RNA binding binding nucleic acid binding	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 protein biosynthetic process regulation of translation, ncRNA-mediated protein metabolic process regulation of protein metabolic process translation regulation of translation 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR010920	LSM domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR005001	RNA-binding protein Hfq	Family
A, B, C, D, E A, B, C, D, E, F	IPR047575	Sm domain	Domain

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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.