Annotations: 5SZD

Crystal structure of Aquifex aeolicus Hfq at 1.5A

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)
L	d5szdl1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
L	d5szdl2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
K	d5szdk1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
K	d5szdk2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
J	d5szdj1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
J	d5szdj2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
I	d5szdi1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
I	d5szdi2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
H	d5szdh1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
H	d5szdh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
G	d5szdg1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
G	d5szdg2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
F	d5szdf1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
F	d5szdf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
E	d5szde_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
D	d5szdd_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
C	d5szdc1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
C	d5szdc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
B	d5szdb1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
B	d5szdb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
A	d5szda1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)
A	d5szda2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus VF5 ) [TaxId: 224324 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058979	3000419	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058979	3000419	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058979	3000419	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058979	3000419	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058979	3000419	SCOP2B (2022-06-29)
G	SCOP2 Family	Pleiotropic translational regulator Hfq	8058978	4002164	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	Sm-like ribonucleoproteins	8058979	3000419	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058979	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058979	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058979	3000419	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058979	3000419	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058979	3000419	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058979	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)
L	Glyco_hydro_77	e5szdL1	A: beta barrels	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.2)
K	Glyco_hydro_77	e5szdK1	A: beta barrels	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.2)
J	Glyco_hydro_77	e5szdJ1	A: beta barrels	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.2)
I	Glyco_hydro_77	e5szdI1	A: beta barrels	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.2)
H	Glyco_hydro_77	e5szdH1	A: beta barrels	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.2)
G	Glyco_hydro_77	e5szdG1	A: beta barrels	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.2)
F	Glyco_hydro_77	e5szdF1	A: beta barrels	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.2)
E	Glyco_hydro_77	e5szdE1	A: beta barrels	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.2)
D	Glyco_hydro_77	e5szdD1	A: beta barrels	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.2)
C	Glyco_hydro_77	e5szdC1	A: beta barrels	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.2)
B	Glyco_hydro_77	e5szdB1	A: beta barrels	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.2)
A	Glyco_hydro_77	e5szdA1	A: beta barrels	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Provenance Source (Version)
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)
J	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)
H	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)
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, G, H, I, J, K, L	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, G, H, I, J, K, L	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 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, G, H, I, J, K, L	IPR010920	LSM domain superfamily	Homologous Superfamily
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