3NDB | pdb_00003ndb

Crystal structure of a signal sequence bound to the signal recognition particle

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)
B	SCOP2B Superfamily	Simibi-like P-loop NTPases	8017987	3002018	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SRP/SRP receptor N-terminal domain-like	8056551	3001834	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SRP19	8041324	3000831	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)
B	TetR_N	e3ndbB2	A: a/b three-layered sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: L30e-like	T: L30e-like	F: TetR_N	ECOD (v294.1)
B	GTP_EFTU, MMR_HSR1	e3ndbB4	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: GTP_EFTU, MMR_HSR1	ECOD (v294.1)
A	Pkinase, ABC1	e3ndbA1	A: a/b three-layered sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: L30e-like	T: L30e-like	F: Pkinase, ABC1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.20.120.140	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	SRP54, nucleotide-binding domain	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.260.30	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	Signal recognition particle, SRP54 subunit, M-domain	CATH (4.3.0)
A	3.30.56.30	Alpha Beta	2-Layer Sandwich	Phenylalanyl-tRNA Synthetase	Chain B, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00448	SRP54-type protein, GTPase domain (SRP54)	SRP54-type protein, GTPase domain	This family includes relatives of the G-domain of the SRP54 family of proteins.	Domain
B	PF02978	Signal peptide binding domain (SRP_SPB)	Signal peptide binding domain		Domain
B	PF02881	SRP54-type protein, helical bundle domain (SRP54_N)	SRP54-type protein, helical bundle domain		Domain
A	PF01922	SRP19 protein (SRP19)	SRP19 protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Signal recognition 54 kDa protein	RNA binding 7S RNA binding binding nucleic acid binding molecular adaptor activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding RNA binding 7S RNA binding binding nucleic acid binding molecular adaptor activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane establishment of localization protein targeting to membrane localization SRP-dependent cotranslational protein targeting to membrane establishment of protein localization to organelle cotranslational protein targeting to membrane cellular process establishment of protein localization to endoplasmic reticulum protein targeting to ER	signal recognition particle protein-containing complex cellular anatomical structure intracellular anatomical structure ribonucleoprotein complex cytoplasm
C [auth M]	SRP RNA	-	-	-
A	Signal recognition particle 19 kDa protein	RNA binding 7S RNA binding binding nucleic acid binding	establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane establishment of localization protein targeting to membrane localization SRP-dependent cotranslational protein targeting to membrane establishment of protein localization to organelle cotranslational protein targeting to membrane cellular process establishment of protein localization to endoplasmic reticulum protein targeting to ER	signal recognition particle protein-containing complex cellular anatomical structure intracellular anatomical structure ribonucleoprotein complex cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR000897	Signal recognition particle, SRP54 subunit, GTPase domain	Domain
B	IPR022941	Signal recognition particle, SRP54 subunit	Family
B	IPR036225	SRP/SRP receptor, N-terminal	Homologous Superfamily
B	IPR004125	Signal recognition particle, SRP54 subunit, M-domain	Domain
B	IPR042101	Signal recognition particle SRP54, N-terminal domain superfamily	Homologous Superfamily
B	IPR003593	AAA+ ATPase domain	Domain
B	IPR013822	Signal recognition particle SRP54, helical bundle	Domain
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR036891	Signal recognition particle, SRP54 subunit, M-domain superfamily	Homologous Superfamily
A	IPR002778	Signal recognition particle, SRP19 subunit	Family
A	IPR022938	Signal recognition particle, SRP19 subunit, archaeal-type	Family
A	IPR036521	Signal recognition particle, subunit SRP19-like 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.