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- PDB-2go5: Structure of signal recognition particle receptor (SR) in complex... -

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Basic information

Entry
Database: PDB / ID: 2go5
TitleStructure of signal recognition particle receptor (SR) in complex with signal recognition particle (SRP) and ribosome nascent chain complex
Components
  • (Signal recognition particle ...) x 4
  • (ribosomal protein ...) x 3
  • SRP RNA
  • ribosomal RNA
KeywordsTRANSLATION/RNA / SR / SRP / RIBOSOME / TRANSLATION-RNA COMPLEX
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal recognition particle binding / cotranslational protein targeting to membrane / protein targeting to ER / signal-recognition-particle GTPase ...SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal recognition particle binding / cotranslational protein targeting to membrane / protein targeting to ER / signal-recognition-particle GTPase / XBP1(S) activates chaperone genes / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / cytoplasmic microtubule / SRP-dependent cotranslational protein targeting to membrane / neutrophil chemotaxis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / intracellular protein transport / GDP binding / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / nuclear speck / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / GTP binding / nucleolus / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle receptor, beta subunit / Signal recognition particle receptor beta subunit / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit ...Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle receptor, beta subunit / Signal recognition particle receptor beta subunit / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Small GTPase superfamily, ARF type / Longin-like domain superfamily / Ribosomal protein L23 / 60S ribosomal protein L35 / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Ribosomal protein L25 / Signal recognition particle receptor subunit alpha / Signal recognition particle receptor subunit beta / Signal recognition particle subunit SRP54 / Signal recognition particle 19 kDa protein / Putative 60S ribosomal protein L31 / Large ribosomal subunit protein uL29
Similarity search - Component
Biological speciesCanis sp. (mammal)
Homo sapiens (human)
Mus musculus (house mouse)
Triticum sp. (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsHalic, M. / Gartmann, M. / Schlenker, O. / Mielke, T. / Pool, M.R. / Sinning, I. / Beckmann, R.
CitationJournal: Science / Year: 2006
Title: Signal recognition particle receptor exposes the ribosomal translocon binding site.
Authors: Mario Halic / Marco Gartmann / Oliver Schlenker / Thorsten Mielke / Martin R Pool / Irmgard Sinning / Roland Beckmann /
Abstract: Signal sequences of secretory and membrane proteins are recognized by the signal recognition particle (SRP) as they emerge from the ribosome. This results in their targeting to the membrane by ...Signal sequences of secretory and membrane proteins are recognized by the signal recognition particle (SRP) as they emerge from the ribosome. This results in their targeting to the membrane by docking with the SRP receptor, which facilitates transfer of the ribosome to the translocon. Here, we present the 8 angstrom cryo-electron microscopy structure of a "docking complex" consisting of a SRP-bound 80S ribosome and the SRP receptor. Interaction of the SRP receptor with both SRP and the ribosome rearranged the S domain of SRP such that a ribosomal binding site for the translocon, the L23e/L35 site, became exposed, whereas Alu domain-mediated elongation arrest persisted.
History
DepositionApr 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Remark 999SEQUENCE Residue (A G 124) and Residue (A G 125) are not linked. Distance of O3*-P bond is 4.22. ...SEQUENCE Residue (A G 124) and Residue (A G 125) are not linked. Distance of O3*-P bond is 4.22. Residue (A C 221) and Residue (A G 222) are not linked. Distance of O3*-P bond is 3.26. Residue (1 SER 0) and Residue (1 MET 1) are not linked. Distance of C-N bond is 17.58. Residue (1 GLY 27) and Residue (1 PRO 28) are not linked. Distance of C-N bond is 7.21. Residue (1 LEU 52) and Residue (1 THR 53) are not linked. Distance of C-N bond is 5.58.

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Assembly

Deposited unit
A: SRP RNA
9: ribosomal RNA
B: Signal recognition particle 19 kDa protein (SRP19)
W: Signal recognition particle 54 kDa protein (SRP54)
1: Signal recognition particle receptor alpha subunit (SR a)
2: Signal recognition particle receptor beta subunit (SR b)
5: ribosomal protein L35
4: ribosomal protein L23
6: ribosomal protein L31


Theoretical massNumber of molelcules
Total (without water)185,7459
Polymers185,7459
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules A9

#1: RNA chain SRP RNA


Mass: 41199.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis sp. (mammal)
#2: RNA chain ribosomal RNA


Mass: 29170.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum sp. (plant)

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Signal recognition particle ... , 4 types, 4 molecules BW12

#3: Protein Signal recognition particle 19 kDa protein (SRP19)


Mass: 12561.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis sp. (mammal) / References: UniProt: Q5RBR1*PLUS
#4: Protein Signal recognition particle 54 kDa protein (SRP54)


Mass: 12473.440 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis sp. (mammal) / References: UniProt: P61010
#5: Protein Signal recognition particle receptor alpha subunit (SR a)


Mass: 21329.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P08240
#6: Protein Signal recognition particle receptor beta subunit (SR b)


Mass: 23536.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P47758

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Ribosomal protein ... , 3 types, 3 molecules 546

#7: Protein ribosomal protein L35


Mass: 14401.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum sp. (plant) / References: UniProt: Q8L805
#8: Protein ribosomal protein L23


Mass: 16920.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum sp. (plant) / References: UniProt: O81229*PLUS
#9: Protein ribosomal protein L31


Mass: 14152.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum sp. (plant) / References: UniProt: Q5XLD9*PLUS

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SR-SRP-RNC COMPLEX / Type: RIBOSOME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm
Image recordingFilm or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.4 Å / Resolution method: FSC 0.5 CUT-OFF / Symmetry type: POINT
RefinementHighest resolution: 7.4 Å
Refinement stepCycle: LAST / Highest resolution: 7.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6061 4663 0 0 10724

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