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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 / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal recognition particle / cotranslational protein targeting to membrane / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / protein targeting to ER / 7S RNA binding ...SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal recognition particle / cotranslational protein targeting to membrane / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / protein targeting to ER / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane, translocation / phototransduction / SRP-dependent cotranslational protein targeting to membrane / visual perception / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / neutrophil chemotaxis / chloroplast / G protein-coupled receptor activity / GDP binding / cytosolic large ribosomal subunit / membrane => GO:0016020 / cytoplasmic translation / nuclear body / rRNA binding / nuclear speck / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / nucleus / cytosol
Similarity search - Function
Rhodopsin, N-terminal domain superfamily / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit ...Rhodopsin, N-terminal domain superfamily / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / 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 / 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. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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 19 kDa protein / Signal recognition particle subunit SRP54 / Rhodopsin / Putative 60S ribosomal protein L31 / Large ribosomal subunit protein uL29
Similarity search - Component
Biological speciesTRITICUM SP. (plant)
TRITICUM SP (plant)
CANIS SP. (mammal)
HOMO SAPIENS (human)
HALOARCULA MARISMORTUI (Halophile)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å
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.
History
DepositionAug 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Database references / Structure summary
Category: citation / em_image_scans / entity
Item: _citation.journal_id_ISSN / _citation.page_first ..._citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.src_method
Revision 1.4Apr 10, 2019Group: Data collection / Database references / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / diffrn / diffrn_radiation / diffrn_radiation_wavelength / entity_src_nat / struct_ref
Item: _struct_ref.db_name
Revision 1.5May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high

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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
Polymers248,0048
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-45.2 kcal/mol
Surface area123400 Å2
MethodPQS

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Components

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

#2: Protein RIBOSOMAL PROTEIN L35


Mass: 14401.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRITICUM SP. (plant) / References: UniProt: Q8L805
#3: Protein RIBOSOMAL PROTEIN L31


Mass: 14152.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 method: isolated from a natural source / Source: (natural) CANIS SP. (mammal)
#8: RNA chain RIBOSOMAL RNA


Mass: 90695.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile)

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

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


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


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

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Protein / Protein/peptide , 2 types, 2 molecules 4S

#1: Protein 60S RIBOSOMAL PROTEIN L23


Mass: 16920.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRITICUM SP. (plant) / References: UniProt: O81229*PLUS
#6: Protein/peptide SIGNAL SEQUENCE


Mass: 1992.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CANIS SP. (mammal) / References: UniProt: Q1WHN3*PLUS

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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: 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
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: 3000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.7 Å / Resolution method: FSC 0.5 CUT-OFF / Symmetry type: POINT
RefinementHighest resolution: 8.7 Å
Refinement stepCycle: LAST / Highest resolution: 8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 8756 0 0 15110

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