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- PDB-2j37: MODEL OF MAMMALIAN SRP BOUND TO 80S RNCS -

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Basic information

Entry
Database: PDB / ID: 2j37
TitleMODEL OF MAMMALIAN SRP BOUND TO 80S RNCS
Components
  • (RIBOSOMAL PROTEIN ...) x 2
  • (SIGNAL RECOGNITION PARTICLE ...) x 2
  • 60S RIBOSOMAL PROTEIN L23
  • RIBOSOMAL RNA
  • SIGNAL SEQUENCE
  • SRP RNA
KeywordsRIBOSOME / SRP / TRANSLATION/RNA
Function / homologyNucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L29/L35 superfamily / Signal recognition particle, SRP54 subunit, M-domain / Ribosomal protein L23/L25, N-terminal / Signal recognition particle, SRP54 subunit, eukaryotic / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L25/L23 / Signal recognition particle, SRP54 subunit, helical bundle / GPCR, rhodopsin-like, 7TM / Rhodopsin, N-terminal ...Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L29/L35 superfamily / Signal recognition particle, SRP54 subunit, M-domain / Ribosomal protein L23/L25, N-terminal / Signal recognition particle, SRP54 subunit, eukaryotic / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L25/L23 / Signal recognition particle, SRP54 subunit, helical bundle / GPCR, rhodopsin-like, 7TM / Rhodopsin, N-terminal / Ribosomal protein L23 / Signal recognition particle, SRP54 subunit / Ribosomal protein L31e domain superfamily / P-loop containing nucleoside triphosphate hydrolase / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / Signal recognition particle, SRP54 subunit, M-domain superfamily / Rhodopsin, N-terminal domain superfamily / 7 transmembrane receptor (rhodopsin family) / Ribosomal protein L23 / SRP54-type protein, GTPase domain / Ribosomal L29 protein / Ribosomal protein L31e / SRP19 protein / SRP54-type protein, helical bundle domain / Signal peptide binding domain / Ribosomal protein L23, N-terminal domain / AAA+ ATPase domain / Ribosomal protein L29/L35 / Ribosomal protein L23 signature. / SRP54-type proteins GTP-binding domain signature. / SRP-dependent cotranslational protein targeting to membrane / G-protein coupled receptors family 1 profile. / Ribosomal protein L23/L25, conserved site / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Ribosomal protein L31e / Signal recognition particle, SRP54 subunit, GTPase domain / G protein-coupled receptor, rhodopsin-like / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / cotranslational protein targeting to membrane / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane, translocation / signal recognition particle / 7S RNA binding / G-protein coupled receptor activity / ribonucleoprotein complex binding / SRP-dependent cotranslational protein targeting to membrane / phototransduction / GDP binding / ribosome / drug binding / structural constituent of ribosome / translation / GTPase activity / response to drug / GTP binding / nucleolus / RNA binding / integral component of membrane / nucleus / cytosol / | / Ribosomal protein L25 / Signal recognition particle 19 kDa protein / Signal recognition particle 54 kDa protein / Rhodopsin / Putative 60S ribosomal protein L31 / 60S ribosomal protein L35
Function and homology information
Specimen sourceTRITICUM SP. (plant)
TRITICUM SP (plant)
CANIS SP. (mammal)
HOMO SAPIENS (human)
HALOARCULA MARISMORTUI (Halophile)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8.7 Å resolution
AuthorsHalic, M. / Blau, M. / Becker, T. / Mielke, T. / Pool, M.R. / Wild, K. / Sinning, I. / Beckmann, R.
CitationJournal: Nature / Year: 2006
Title: Following the signal sequence from ribosomal tunnel exit to signal recognition particle.
Authors: Mario Halic / Michael Blau / Thomas Becker / Thorsten Mielke / Martin R Pool / Klemens Wild / Irmgard Sinning / Roland Beckmann
Abstract: Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal ...Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal recognition particle (SRP), which results in targeting of the ribosome-nascent-chain complex to the protein-conducting channel at the membrane. Here we present an ensemble of structures at subnanometre resolution, revealing the signal sequence both at the ribosomal tunnel exit and in the bacterial and eukaryotic ribosome-SRP complexes. Molecular details of signal sequence interaction in both prokaryotic and eukaryotic complexes were obtained by fitting high-resolution molecular models. The signal sequence is presented at the ribosomal tunnel exit in an exposed position ready for accommodation in the hydrophobic groove of the rearranged SRP54 M domain. Upon ribosome binding, the SRP54 NG domain also undergoes a conformational rearrangement, priming it for the subsequent docking reaction with the NG domain of the SRP receptor. These findings provide the structural basis for improving our understanding of the early steps of co-translational protein sorting.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 18, 2006 / Release: Nov 8, 2006
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 8, 2006Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Mar 7, 2018Structure modelData collection / Database references / Structure summarycitation / em_image_scans / entity_citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.src_method

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Assembly

Deposited unit
4: 60S RIBOSOMAL PROTEIN L23
5: RIBOSOMAL PROTEIN L35
6: RIBOSOMAL PROTEIN L31
A: SRP RNA
B: SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN (SRP19)
S: SIGNAL SEQUENCE
W: SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN (SRP54)
Z: RIBOSOMAL RNA


Theoretical massNumber of molelcules
Total (without water)248,0048
Polyers248,0048
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)11800
ΔGint (kcal/M)-45.2
Surface area (Å2)123400
MethodPQS

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Components

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Protein/peptide , 2 types, 2 molecules 4S

#1: Protein/peptide 60S RIBOSOMAL PROTEIN L23 /


Mass: 16920.203 Da / Num. of mol.: 1 / Source: (natural) TRITICUM SP. (plant) / References: UniProt:2J37, UniProt:O81229*PLUS
#6: Protein/peptide SIGNAL SEQUENCE /


Mass: 1992.362 Da / Num. of mol.: 1 / References: UniProt:Q1WHN3*PLUS

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RIBOSOMAL PROTEIN ... , 2 types, 2 molecules 56

#2: Protein/peptide RIBOSOMAL PROTEIN L35 / Ribosome


Mass: 14401.041 Da / Num. of mol.: 1 / Source: (natural) TRITICUM SP. (plant) / References: UniProt:Q8L805
#3: Protein/peptide RIBOSOMAL PROTEIN L31 / Ribosome


Mass: 14152.365 Da / Num. of mol.: 1 / Source: (natural) TRITICUM SP (plant) / References: UniProt:Q5XLD9*PLUS

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RNA chain , 2 types, 2 molecules AZ

#4: RNA chain SRP RNA


Mass: 41504.750 Da / Num. of mol.: 1 / Source: (natural) CANIS SP. (mammal)
#8: RNA chain RIBOSOMAL RNA /


Mass: 90695.906 Da / Num. of mol.: 1 / Source: (natural) HALOARCULA MARISMORTUI (Halophile)

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SIGNAL RECOGNITION PARTICLE ... , 2 types, 2 molecules BW

#5: Protein/peptide SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN (SRP19)


Mass: 12561.688 Da / Num. of mol.: 1 / Source: (natural) HOMO SAPIENS (human) / References: UniProt:P09132
#7: Protein/peptide SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN (SRP54)


Mass: 55775.672 Da / Num. of mol.: 1 / Source: (natural) CANIS SP. (mammal) / References: UniProt:P61010

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: SRP BOUND TO 80S RNCS / 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
MicroscopyMicroscope model: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

SymmetryPoint symmetry: C1
3D reconstructionResolution: 8.7 Å / Resolution method: FSC 0.5 CUT-OFF / Symmetry type: POINT
Least-squares processHighest resolution: 8 Å
Refine hist #LASTHighest resolution: 8 Å
Number of atoms included #LASTProtein: 6354 / Nucleic acid: 8756 / Ligand: 0 / Solvent: 0 / Total: 15110

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