3GKU | pdb_00003gku

Crystal structure of a probable RNA-binding protein from Clostridium symbiosum ATCC 14940

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	R3H	e3gkuA3	A: a+b two layers	X: R3H domain-like	H: R3H domain (From Topology)	T: R3H domain	F: R3H	ECOD (1.6)
A	KH_4	e3gkuA2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: KH_4	ECOD (1.6)
A	Jag_N	e3gkuA1	A: a+b two layers	X: Dodecin subunit-like	H: Probable RNA-binding protein N-terminal domain (From Topology)	T: Probable RNA-binding protein N-terminal domain	F: Jag_N	ECOD (1.6)
B	R3H	e3gkuB8	A: a+b two layers	X: R3H domain-like	H: R3H domain (From Topology)	T: R3H domain	F: R3H	ECOD (1.6)
B	KH_4	e3gkuB7	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: KH_4	ECOD (1.6)
B	Jag_N	e3gkuB9	A: a+b two layers	X: Dodecin subunit-like	H: Probable RNA-binding protein N-terminal domain (From Topology)	T: Probable RNA-binding protein N-terminal domain	F: Jag_N	ECOD (1.6)
C	KH_4	e3gkuC2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: KH_4	ECOD (1.6)
C	Jag_N	e3gkuC1	A: a+b two layers	X: Dodecin subunit-like	H: Probable RNA-binding protein N-terminal domain (From Topology)	T: Probable RNA-binding protein N-terminal domain	F: Jag_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.30.80	Alpha Beta	2-Layer Sandwich	Defensin A-like	probable RNA-binding protein from clostridium symbiosum atcc 14940	CATH (4.3.0)
A	3.30.300.20	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
A	3.30.1370.50	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
B	3.30.30.80	Alpha Beta	2-Layer Sandwich	Defensin A-like	probable RNA-binding protein from clostridium symbiosum atcc 14940	CATH (4.3.0)
B	3.30.300.20	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
B	3.30.1370.50	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
C	3.30.30.80	Alpha Beta	2-Layer Sandwich	Defensin A-like	probable RNA-binding protein from clostridium symbiosum atcc 14940	CATH (4.3.0)
C	3.30.300.20	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF13083	KhpA/KhpB, KH domain (KH_KhpA-B)	KhpA/KhpB, KH domain	The K homology domain is a common RNA-binding motif present in one or multiple copies in both prokaryotic and eukaryotic regulatory proteins. These motifs may act cooperatively to bind RNA in the case of multiple motifs, or independently in the case ...	The K homology domain is a common RNA-binding motif present in one or multiple copies in both prokaryotic and eukaryotic regulatory proteins. These motifs may act cooperatively to bind RNA in the case of multiple motifs, or independently in the case of single KH motif proteins. The structure of the prokaryotic KH domain consists of a two-layer alpha/beta fold in the arrangement alpha/beta(2)/alpha/beta. This entry represents the KH domain from RNA-binding protein KhpA and KhpB (also known as Jag or EloR) [1]. KhpA is a single-KH domain protein while KhpB also has a Jag-N domain (Pfam:PF14804) of unknown function and a R3H domain (Pfam:PF01424) at the C-terminal [1].	Domain
A, B, C	PF14804	Jag N-terminus (Jag_N)	Jag N-terminus	This domain is found at the N-terminus of proteins containing Pfam:PF13083 and Pfam:PF01424, including the jag proteins.	Domain
A, B, C	PF01424	R3H domain (R3H)	R3H domain	The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Probable RNA-binding protein	RNA binding binding nucleic acid binding	developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular component organization cell wall organization or biogenesis cell wall organization developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process metabolic process glycosaminoglycan biosynthetic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR038008	Jag, KH domain	Domain
A, B, C	IPR034079	RNA-binding protein KhpB, R3H domain	Domain
A, B, C	IPR039247	RNA-binding protein KhpB	Family
A, B, C	IPR032782	RNA-binding protein KhpB, N-terminal	Domain
A, B, C	IPR036867	R3H domain superfamily	Homologous Superfamily
A, B, C	IPR001374	R3H domain	Domain
A, B, C	IPR015946	K homology domain-like, alpha/beta	Homologous Superfamily
A, B, C	IPR038247	Jag, N-terminal domain 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.