6O1K | pdb_00006o1k

Architectural principles for Hfq/Crc-mediated regulation of gene expression. Hfq-Crc-amiE 2:2:2 complex (core complex)

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)
D	d6o1kd_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	Pleiotropic translational regulator Hfq	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
H	d6o1kh_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	Pleiotropic translational regulator Hfq	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
I	d6o1ki_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	Pleiotropic translational regulator Hfq	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
J	d6o1kj_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	Pleiotropic translational regulator Hfq	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
M	d6o1km_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	Pleiotropic translational regulator Hfq	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
N	d6o1kn_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	Pleiotropic translational regulator Hfq	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
L	d6o1kl_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	Pleiotropic translational regulator Hfq	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
K	d6o1kk_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	Pleiotropic translational regulator Hfq	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
G	d6o1kg_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	Pleiotropic translational regulator Hfq	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
F	d6o1kf_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	Pleiotropic translational regulator Hfq	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
E	d6o1ke_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	Pleiotropic translational regulator Hfq	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
C	d6o1kc_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Pleiotropic translational regulator Hfq	Pleiotropic translational regulator Hfq	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
B	d6o1kb1	Alpha and beta proteins (a+b)	DNase I-like	DNase I-like	automated matches	automated matches	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d6o1kb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
A	d6o1ka1	Alpha and beta proteins (a+b)	DNase I-like	DNase I-like	automated matches	automated matches	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
A	d6o1ka2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Sm-like ribonucleoproteins	8032703	3000419	SCOP2B (2022-06-29)
N	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)
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)
C	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)
D	LSM	e6o1kD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
H	LSM	e6o1kH1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
I	LSM	e6o1kI1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
J	LSM	e6o1kJ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
M	LSM	e6o1kM1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
N	LSM	e6o1kN1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
L	LSM	e6o1kL1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
K	LSM	e6o1kK1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
G	LSM	e6o1kG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F	LSM	e6o1kF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E	LSM	e6o1kE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
C	LSM	e6o1kC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
B	Exo_endo_phos	e6o1kB1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)
A	Exo_endo_phos	e6o1kA1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: DNase I-like (From Topology)	T: DNase I-like	F: Exo_endo_phos	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
M	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
N	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)
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)
C	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
C, D, E, F, G C, D, E, F, G, H, I, J, K, L, M, N	PF17209	Hfq protein (Hfq)	Hfq protein		Domain
A, B	PF03372	Endonuclease/Exonuclease/phosphatase family (Exo_endo_phos)	Endonuclease/Exonuclease/phosphatase family	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3. ...	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3.1.21.1 e.g. Swiss:P24855, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56 Swiss:O43426, Sphingomyelinase EC:3.1.4.12 Swiss:P11889 and Nocturnin Swiss:O35710.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
O, P	RNA (5'-R(APAPAPAPAPUPAPAPCPAPAPCPAPAPGPAPGPG)-3')	-	-	-
C, D, E, F, G C, D, E, F, G, H, I, J, K, L, M, N	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
A, B	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
C, D, E, F, G C, D, E, F, G, H, I, J, K, L, M, N	IPR010920	LSM domain superfamily	Homologous Superfamily
C, D, E, F, G C, D, E, F, G, H, I, J, K, L, M, N	IPR005001	RNA-binding protein Hfq	Family
C, D, E, F, G C, D, E, F, G, H, I, J, K, L, M, N	IPR047575	Sm domain	Domain
A, B	IPR005135	Endonuclease/exonuclease/phosphatase	Domain
A, B	IPR037493	Exodeoxyribonuclease III-like	Family
A, B	IPR004808	AP endonuclease 1	Family
A, B	IPR036691	Endonuclease/exonuclease/phosphatase 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.