4UE5 | pdb_00004ue5

Structural basis for targeting and elongation arrest of Bacillus signal recognition particle

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	SCOP2 Family	Signal recognition particle alu RNA binding heterodimer, SRP9/14	8077810	4001167	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Signal recognition particle alu RNA binding heterodimer, SRP9/14	8077811	3000976	SCOP2 (2022-06-29)
C	SCOP2 Family	RNA-binding signal recognition particle 68-like	8046406	4005065	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	TPR-like	8053750	3001345	SCOP2 (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		e4ue5B1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: RNA polymerase I subunits A49/A34.5 dimerization domains	F:	ECOD (v294.1)
C		e4ue5C1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: RNA polymerase I subunits A49/A34.5 dimerization domains	F:	ECOD (v294.1)
D	Fumble	e4ue5D1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: Fumble	ECOD (v294.1)
E		e4ue5E1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: RNA polymerase I subunits A49/A34.5 dimerization domains	F:	ECOD (v294.1)
F		e4ue5F1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: RNA polymerase I subunits A49/A34.5 dimerization domains	F:	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF02290	Signal recognition particle 14kD protein (SRP14)	Signal recognition particle 14kD protein	The signal recognition particle (SRP) is a multimeric protein involved in targeting secretory proteins to the rough endoplasmic reticulum membrane. SRP14 and SRP9 form a complex essential for SRP RNA binding.	Domain
C	PF16969	RNA-binding signal recognition particle 68 (SRP68)	RNA-binding signal recognition particle 68	-	Family
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
D	PF02978	Signal peptide binding domain (SRP_SPB)	Signal peptide binding domain		Domain
D	PF02881	SRP54-type protein, helical bundle domain (SRP54_N)	SRP54-type protein, helical bundle domain		Domain
E	PF05486	Signal recognition particle 9 kDa protein (SRP9) (SRP9-21)	Signal recognition particle 9 kDa protein (SRP9)	This family consists of several eukaryotic SRP9 proteins. SRP9 together with the Alu-homologous region of 7SL RNA and SRP14 comprise the "Alu domain" of SRP, which mediates pausing of synthesis of ribosome associated nascent polypeptides that have be ...	This family consists of several eukaryotic SRP9 proteins. SRP9 together with the Alu-homologous region of 7SL RNA and SRP14 comprise the "Alu domain" of SRP, which mediates pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [1]. This family also contains the homologous fungal SRP21 [2].	Domain
F	PF01922	SRP19 protein (SRP19)	SRP19 protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	7S RNA	-	-	-
B	SRP14	endoplasmic reticulum signal peptide binding signal sequence binding binding peptide binding RNA binding 7S RNA 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol signal recognition particle protein-containing complex signal recognition particle, endoplasmic reticulum targeting ribonucleoprotein complex
C	SIGNAL RECOGNITION PARTICLE SUBUNIT SRP68	endoplasmic reticulum signal peptide binding signal sequence binding binding peptide binding ribonucleoprotein complex binding protein-containing complex binding signal recognition particle binding RNA binding 7S RNA 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle membraneless organelle nuclear lumen signal recognition particle protein-containing complex signal recognition particle, endoplasmic reticulum targeting ribonucleoprotein complex endoplasmic reticulum endomembrane system
D	SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN	endoplasmic reticulum signal peptide binding signal sequence binding binding peptide binding ribonucleoprotein complex binding protein-containing complex binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding endoplasmic reticulum signal peptide binding signal sequence binding binding peptide binding ribonucleoprotein complex binding protein-containing complex 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 GDP binding RNA binding 7S RNA binding nucleic acid 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	cell chemotaxis cellular response to stimulus chemotaxis response to stimulus neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis immune system process granulocyte chemotaxis response to chemical myeloid leukocyte migration cell chemotaxis cellular response to stimulus chemotaxis response to stimulus neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis immune system process granulocyte chemotaxis response to chemical myeloid leukocyte migration cell migration cellular process cell motility leukocyte chemotaxis locomotion developmental process myeloid leukocyte differentiation cellular developmental process hemopoiesis cell development granulocyte differentiation myeloid cell differentiation cell differentiation anatomical structure development leukocyte differentiation localization establishment of protein localization establishment of protein localization to organelle protein targeting establishment of localization establishment of protein localization to endoplasmic reticulum protein targeting to ER cellular localization SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition protein-containing complex organization establishment of protein localization to membrane localization within membrane protein targeting to membrane cellular component organization cellular component biogenesis cellular component assembly SRP-dependent cotranslational protein targeting to membrane protein-containing complex assembly cotranslational protein targeting to membrane cellular component organization or biogenesis multicellular organismal process digestive system development gland development animal organ development exocrine pancreas development multicellular organism development pancreas development exocrine system development system development transport protein transmembrane transport establishment of localization in cell intracellular protein localization intracellular protein transmembrane transport intracellular transport transmembrane transport protein transport macromolecule localization SRP-dependent cotranslational protein targeting to membrane, translocation intracellular protein transport	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytoplasm cytosol signal recognition particle protein-containing complex signal recognition particle, endoplasmic reticulum targeting ribonucleoprotein complex endoplasmic reticulum endomembrane system
E	SRP9	RNA binding 7S RNA binding binding nucleic acid binding	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of translational elongation negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of translational elongation negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process negative regulation of translational elongation regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process translational elongation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process 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 signal recognition particle protein-containing complex signal recognition particle, endoplasmic reticulum targeting ribonucleoprotein complex
F	SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN	RNA binding 7S RNA binding binding nucleic acid binding	establishment of protein localization cellular localization SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition protein-containing complex organization establishment of protein localization to membrane protein targeting localization within membrane establishment of localization protein targeting to membrane cellular component organization cellular component biogenesis localization cellular component assembly SRP-dependent cotranslational protein targeting to membrane establishment of protein localization to organelle establishment of protein localization cellular localization SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition protein-containing complex organization establishment of protein localization to membrane protein targeting localization within membrane establishment of localization protein targeting to membrane cellular component organization cellular component biogenesis localization cellular component assembly SRP-dependent cotranslational protein targeting to membrane establishment of protein localization to organelle protein-containing complex assembly cotranslational protein targeting to membrane cellular process cellular component organization or biogenesis establishment of protein localization to endoplasmic reticulum protein targeting to ER	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen signal recognition particle protein-containing complex signal recognition particle, endoplasmic reticulum targeting ribonucleoprotein complex cytoplasm nucleoplasm
G [auth S]	SIGNAL SEQUENCE	G protein-coupled photoreceptor activity molecular transducer activity photoreceptor activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity vitamin binding binding retinal binding isoprenoid binding retinoid binding lipid binding 11-cis retinal binding small molecule binding G protein-coupled photoreceptor activity molecular transducer activity photoreceptor activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity vitamin binding binding retinal binding isoprenoid binding retinoid binding lipid binding 11-cis retinal binding small molecule binding cation binding ion binding metal ion binding	cellular response to stimulus response to light stimulus regulation of cellular process response to stimulus signaling detection of abiotic stimulus cellular response to environmental stimulus cell communication cellular response to light stimulus signal transduction detection of light stimulus phototransduction detection of external stimulus regulation of biological process cellular response to stimulus response to light stimulus regulation of cellular process response to stimulus signaling detection of abiotic stimulus cellular response to environmental stimulus cell communication cellular response to light stimulus signal transduction detection of light stimulus phototransduction detection of external stimulus regulation of biological process biological regulation detection of visible light response to external stimulus cellular response to radiation detection of stimulus response to radiation response to abiotic stimulus cellular process G protein-coupled receptor signaling pathway cellular response to abiotic stimulus G protein-coupled opsin signaling pathway phototransduction, visible light absorption of visible light light absorption multicellular organismal process sensory perception of light stimulus system process sensory perception nervous system process visual perception	membrane-bounded organelle non-motile cilium membrane plasma membrane cilium 9+0 non-motile cilium neuron projection ciliary membrane photoreceptor outer segment membrane photoreceptor outer segment plasma membrane bounded cell projection cell periphery cell projection bounding membrane of organelle membrane-bounded organelle non-motile cilium membrane plasma membrane cilium 9+0 non-motile cilium neuron projection ciliary membrane photoreceptor outer segment membrane photoreceptor outer segment plasma membrane bounded cell projection cell periphery cell projection bounding membrane of organelle cellular anatomical structure photoreceptor cell cilium organelle plasma membrane region organelle membrane cell projection membrane photoreceptor disc membrane photoreceptor inner segment membrane photoreceptor inner segment

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR003210	Signal recognition particle, SRP14 subunit	Family
B	IPR009018	Signal recognition particle, SRP9/SRP14 subunit	Homologous Superfamily
C	IPR026258	Signal recognition particle subunit SRP68	Family
C	IPR038253	SRP68, N-terminal domain superfamily	Homologous Superfamily
C	IPR034652	Signal recognition particle subunit SRP68, RNA-binding domain	Domain
D	IPR000897	Signal recognition particle, SRP54 subunit, GTPase domain	Domain
D	IPR004125	Signal recognition particle, SRP54 subunit, M-domain	Domain
D	IPR003593	AAA+ ATPase domain	Domain
D	IPR013822	Signal recognition particle SRP54, helical bundle	Domain
D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D	IPR022941	Signal recognition particle, SRP54 subunit	Family
D	IPR036225	SRP/SRP receptor, N-terminal	Homologous Superfamily
D	IPR042101	Signal recognition particle SRP54, N-terminal domain superfamily	Homologous Superfamily
D	IPR006325	Signal recognition particle, SRP54 subunit, eukaryotic	Family
D	IPR036891	Signal recognition particle, SRP54 subunit, M-domain superfamily	Homologous Superfamily
E	IPR008832	Signal recognition particle SRP9	Family
E	IPR009018	Signal recognition particle, SRP9/SRP14 subunit	Homologous Superfamily
E	IPR039432	SRP9 domain	Domain
E	IPR039914	Signal recognition particle SRP9-like	Family
F	IPR002778	Signal recognition particle, SRP19 subunit	Family
F	IPR036521	Signal recognition particle, subunit SRP19-like superfamily	Homologous Superfamily
G [auth S]	IPR000732	Rhodopsin	Family
G [auth S]	IPR027430	Visual pigments (opsins) retinal binding site	Binding Site
G [auth S]	IPR019477	Rhodopsin, N-terminal	Domain
G [auth S]	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
G [auth S]	IPR050125	G-protein coupled receptor opsins	Family
G [auth S]	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
G [auth S]	IPR001760	Opsin	Family