4NL3 | pdb_00004nl3

Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNA

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	d4nl3l_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
K	d4nl3k_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
J [auth I]	d4nl3i_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
I [auth H]	d4nl3h_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
H [auth G]	d4nl3g_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
G [auth J]	d4nl3j_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
F	d4nl3f_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
E	d4nl3e_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
D [auth C]	d4nl3c_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
C [auth B]	d4nl3b_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
B [auth A]	d4nl3a_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	SCOPe (2.08)
A [auth D]	d4nl3d_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Listeria monocytogenes ) [TaxId: 1639 ],	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	8058965	3000419	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058965	3000419	SCOP2B (2022-06-29)
J [auth I]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058965	3000419	SCOP2B (2022-06-29)
I [auth H]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058965	3000419	SCOP2B (2022-06-29)
H [auth G]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058965	3000419	SCOP2B (2022-06-29)
G [auth J]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058965	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058965	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058965	3000419	SCOP2B (2022-06-29)
D [auth C]	SCOP2 Family	Pleiotropic translational regulator Hfq	8058964	4002164	SCOP2 (2022-06-29)
D [auth C]	SCOP2 Superfamily	Sm-like ribonucleoproteins	8058965	3000419	SCOP2 (2022-06-29)
C [auth B]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058965	3000419	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058965	3000419	SCOP2B (2022-06-29)
A [auth D]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8058965	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	Hfq_1	e4nl3L1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Hfq_1	ECOD (1.6)
K	Hfq_1	e4nl3K1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Hfq_1	ECOD (1.6)
J [auth I]	Hfq_1	e4nl3I1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Hfq_1	ECOD (1.6)
I [auth H]	Hfq_1	e4nl3H1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Hfq_1	ECOD (1.6)
H [auth G]	Hfq_1	e4nl3G1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Hfq_1	ECOD (1.6)
G [auth J]	Hfq_1	e4nl3J1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Hfq_1	ECOD (1.6)
F	Hfq_1	e4nl3F1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Hfq_1	ECOD (1.6)
E	Hfq_1	e4nl3E1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Hfq_1	ECOD (1.6)
D [auth C]	Hfq_1	e4nl3C1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Hfq_1	ECOD (1.6)
C [auth B]	Hfq_1	e4nl3B1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Hfq_1	ECOD (1.6)
B [auth A]	Hfq_1	e4nl3A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Hfq_1	ECOD (1.6)
A [auth D]	Hfq_1	e4nl3D1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Hfq_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	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 [auth I]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
I [auth H]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
H [auth G]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
G [auth J]	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 [auth C]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C [auth B]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B [auth A]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A [auth D]	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 [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G [auth J], H [auth G], I [auth H], J [auth I], 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
M [auth R], N [auth Z]	5'-R(UPUPUPUPUPU)-3'	-	-	-
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G [auth J], H [auth G], I [auth H], J [auth I], K, L	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 [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G [auth J], H [auth G], I [auth H], J [auth I], K, L	IPR010920	LSM domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G [auth J], H [auth G], I [auth H], J [auth I], K, L	IPR005001	RNA-binding protein Hfq	Family
A [auth D], B [auth A], C [auth B], D [auth C], E, A [auth D], B [auth A], C [auth B], D [auth C], E, F, G [auth J], H [auth G], I [auth H], J [auth I], K, L	IPR047575	Sm domain	Domain

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.