Annotations: 8BVM

Cryo-EM structure of Hfq-Crc-rbsB translation repression complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
O	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	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)
O	Methyltransf_4	e8bvmO1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
M	Methyltransf_4	e8bvmM1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
L	Methyltransf_4	e8bvmL1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
K	Methyltransf_4	e8bvmK1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
J	Methyltransf_4	e8bvmJ1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
I	Methyltransf_4	e8bvmI1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
G	Methyltransf_4	e8bvmG1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
F	Methyltransf_4	e8bvmF1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
E	Methyltransf_4	e8bvmE1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
D	Methyltransf_4	e8bvmD1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
C	Methyltransf_4	e8bvmC1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
B	Methyltransf_4	e8bvmB1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
N	Methyltransf_4	e8bvmN1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
H	Methyltransf_4	e8bvmH1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)
A	Methyltransf_4	e8bvmA1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Methyltransf_4	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
N	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, C, D, E, F B, C, D, E, F, G, I, J, K, L, M, O	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
B, C, D, E, F B, C, D, E, F, G, I, J, K, L, M, O	RNA-binding 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 regulation of protein metabolic process translation protein biosynthetic process regulation of translation protein metabolic process regulation of translation, ncRNA-mediated 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 response to nutrient levels carbon utilization regulation of response to nutrient levels response to stimulus regulation of response to stimulus regulation of carbon utilization signaling quorum sensing cell-cell signaling detection of cell density detection of biotic stimulus response to biotic stimulus cell communication detection of stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
P [auth u]	rbsB mRNA	-	-	-
A, H, N	Catabolite repression control protein	double-stranded DNA 3'-5' DNA exonuclease activity DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity double-stranded DNA exodeoxyribonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity catalytic activity exonuclease activity double-stranded DNA 3'-5' DNA exonuclease activity DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity double-stranded DNA exodeoxyribonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity catalytic activity exonuclease activity cation binding ion binding binding metal ion binding small molecule binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, C, D, E, F B, C, D, E, F, G, I, J, K, L, M, O	IPR010920	LSM domain superfamily	Homologous Superfamily
B, C, D, E, F B, C, D, E, F, G, I, J, K, L, M, O	IPR005001	RNA-binding protein Hfq	Family
B, C, D, E, F B, C, D, E, F, G, I, J, K, L, M, O	IPR047575	Sm domain	Domain
A, H, N	IPR005135	Endonuclease/exonuclease/phosphatase	Domain
A, H, N	IPR037493	Exodeoxyribonuclease III-like	Family
A, H, N	IPR004808	AP endonuclease 1	Family
A, H, N	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	Homologous Superfamily

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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.