4C7O | pdb_00004c7o

The structural basis of FtsY recruitment and GTPase activation by SRP 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)
D	d4c7od1	All alpha proteins	Four-helical up-and-down bundle	Domain of the SRP/SRP receptor G-proteins	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d4c7od2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nitrogenase iron protein-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d4c7od3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4c7ob1	All alpha proteins	Four-helical up-and-down bundle	Domain of the SRP/SRP receptor G-proteins	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4c7ob2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nitrogenase iron protein-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Simibi-like P-loop NTPases	8056575	3002018	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Simibi-like P-loop NTPases	8056575	3002018	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Simibi-like P-loop NTPases	8056567	3002018	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SRP/SRP receptor N-terminal domain-like	8056566	3001834	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Simibi-like P-loop NTPases	8056567	3002018	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SRP/SRP receptor N-terminal domain-like	8056566	3001834	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	CblD	e4c7oD3	A: a/b three-layered sandwiches	X: DEATH domain	H: 40S ribosomal protein S13 N-terminal domain	T: 40S ribosomal protein S13 N-terminal domain	F: CblD	ECOD (v294.1)
B	Vps4_C,AAA_lid_3	e4c7oB2	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: Vps4_C,AAA_lid_3	ECOD (v294.1)
C	SLT_beta	e4c7oC1	A: a/b three-layered sandwiches	X: Suppressor of Fused, C-terminal domain	H: Bacterial enterotoxins	T: Bacterial enterotoxins	F: SLT_beta	ECOD (v294.1)
A	SLT_beta	e4c7oA1	A: a/b three-layered sandwiches	X: Suppressor of Fused, C-terminal domain	H: Bacterial enterotoxins	T: Bacterial enterotoxins	F: SLT_beta	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.120.140	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	SRP54, nucleotide-binding domain	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
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)
C	1.20.120.140	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	SRP54, nucleotide-binding domain	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.20.120.140	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	SRP54, nucleotide-binding domain	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	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, D	PF02881	SRP54-type protein, helical bundle domain (SRP54_N)	SRP54-type protein, helical bundle domain		Domain
A, C	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
A, C	PF02881	SRP54-type protein, helical bundle domain (SRP54_N)	SRP54-type protein, helical bundle domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E	SRP RNA	-	-	-
B, D	SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY	ribonucleoprotein complex binding protein-containing complex binding binding signal recognition particle binding identical protein binding protein binding protein homodimerization activity protein dimerization activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding ribonucleoprotein complex binding protein-containing complex binding binding signal recognition particle binding identical protein binding protein binding protein homodimerization activity protein dimerization 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	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress stringent response cellular process response to starvation cellular response to starvation establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress stringent response cellular process response to starvation cellular response to starvation 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 establishment of protein localization to endoplasmic reticulum protein targeting to ER	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane
A, C	SIGNAL RECOGNITION PARTICLE PROTEIN	RNA binding 7S RNA binding binding nucleic acid binding 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 RNA binding 7S RNA binding binding nucleic acid binding 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol signal recognition particle protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR004390	Signal-recognition particle receptor FtsY	Family
B, D	IPR000897	Signal recognition particle, SRP54 subunit, GTPase domain	Domain
B, D	IPR036225	SRP/SRP receptor, N-terminal	Homologous Superfamily
B, D	IPR042101	Signal recognition particle SRP54, N-terminal domain superfamily	Homologous Superfamily
B, D	IPR003593	AAA+ ATPase domain	Domain
B, D	IPR013822	Signal recognition particle SRP54, helical bundle	Domain
B, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C	IPR000897	Signal recognition particle, SRP54 subunit, GTPase domain	Domain
A, C	IPR022941	Signal recognition particle, SRP54 subunit	Family
A, C	IPR004125	Signal recognition particle, SRP54 subunit, M-domain	Domain
A, C	IPR042101	Signal recognition particle SRP54, N-terminal domain superfamily	Homologous Superfamily
A, C	IPR003593	AAA+ ATPase domain	Domain
A, C	IPR004780	Signal recognition particle protein	Family
A, C	IPR013822	Signal recognition particle SRP54, helical bundle	Domain
A, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C	IPR036891	Signal recognition particle, SRP54 subunit, M-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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.