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- EMDB-1063: Structure of the signal recognition particle interacting with the... -

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Basic information

Entry
Database: EMDB / ID: EMD-1063
TitleStructure of the signal recognition particle interacting with the elongation-arrested ribosome.
Map dataStructure of signal recognition particle interacting with elongation arested ribosome
Sample
  • Sample: 80S RNC-SRP complex fron canis sp.
  • Complex: 80S ribosomeEukaryotic ribosome
  • Ligand: mammalian SRP
  • Ligand: tRNATransfer RNA
Function / homology
Function and homology information


signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / granulocyte differentiation / absorption of visible light / negative regulation of translational elongation / G protein-coupled photoreceptor activity ...signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / granulocyte differentiation / absorption of visible light / negative regulation of translational elongation / G protein-coupled photoreceptor activity / signal recognition particle / photoreceptor inner segment membrane / rhodopsin mediated signaling pathway / 11-cis retinal binding / cotranslational protein targeting to membrane / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane / photoreceptor outer segment membrane / SRP-dependent cotranslational protein targeting to membrane / ribonucleoprotein complex binding / visual perception / neutrophil chemotaxis / photoreceptor disc membrane / GDP binding / secretory granule lumen / ficolin-1-rich granule lumen / nuclear body / nuclear speck / GTPase activity / Neutrophil degranulation / GTP binding / nucleolus / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / extracellular region / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 / Signal recognition particle 9 kDa protein (SRP9) / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily ...Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 / Signal recognition particle 9 kDa protein (SRP9) / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Signal recognition particle protein / Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / 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 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Signal recognition particle protein / Rhodopsin / Signal recognition particle 19 kDa protein / Signal recognition particle subunit SRP54 / Signal recognition particle 14 kDa protein / Signal recognition particle 9 kDa protein
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsHalic M / Beckmann R
CitationJournal: Nature / Year: 2004
Title: Structure of the signal recognition particle interacting with the elongation-arrested ribosome.
Authors: Mario Halic / Thomas Becker / Martin R Pool / Christian M T Spahn / Robert A Grassucci / Joachim Frank / Roland Beckmann /
Abstract: Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. It requires that the translating ribosome be targeted to the membrane by the signal ...Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. It requires that the translating ribosome be targeted to the membrane by the signal recognition particle (SRP), an evolutionarily conserved ribonucleoprotein particle. SRP recognizes signal sequences of nascent protein chains emerging from the ribosome. Subsequent binding of SRP leads to a pause in peptide elongation and to the ribosome docking to the membrane-bound SRP receptor. Here we present the structure of a targeting complex consisting of mammalian SRP bound to an active 80S ribosome carrying a signal sequence. This structure, solved to 12 A by cryo-electron microscopy, enables us to generate a molecular model of SRP in its functional conformation. The model shows how the S domain of SRP contacts the large ribosomal subunit at the nascent chain exit site to bind the signal sequence, and that the Alu domain reaches into the elongation-factor-binding site of the ribosome, explaining its elongation arrest activity.
History
DepositionDec 19, 2003-
Header (metadata) releaseDec 19, 2003-
Map releaseDec 19, 2004-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00019
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.00019
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1ry1
  • Surface level: 0.00014
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1ry1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1063.gif

Downloads & links

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Map

FileDownload / File: emd_1063.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of signal recognition particle interacting with elongation arested ribosome
Voxel sizeX=Y=Z: 3.26 Å
Density
Contour Level1: 0.00055 / Movie #1: 0.00019
Minimum - Maximum-0.000663056 - 0.00216205
Average (Standard dev.)0.0000337914 (±0.000236399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-65-65-65
Dimensions130130130
Spacing130130130
CellA=B=C: 423.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.263.263.26
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z423.800423.800423.800
α/β/γ90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-0.0010.0020.000

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Supplemental data

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Sample components

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Entire : 80S RNC-SRP complex fron canis sp.

EntireName: 80S RNC-SRP complex fron canis sp.
Components
  • Sample: 80S RNC-SRP complex fron canis sp.
  • Complex: 80S ribosomeEukaryotic ribosome
  • Ligand: mammalian SRP
  • Ligand: tRNATransfer RNA

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Supramolecule #1000: 80S RNC-SRP complex fron canis sp.

SupramoleculeName: 80S RNC-SRP complex fron canis sp. / type: sample / ID: 1000 / Oligomeric state: one srp binds one ribosome / Number unique components: 3

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Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 1 / Name.synonym: 80S RNC / Details: q / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Canis lupus familiaris (dog) / synonym: Dog
Molecular weightExperimental: 4 MDa / Theoretical: 4 MDa

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Macromolecule #1: mammalian SRP

MacromoleculeName: mammalian SRP / type: ligand / ID: 1 / Name.synonym: SRP / Details: q / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Canis lupus familiaris (dog) / Strain: beagle / synonym: Dog / Tissue: pancreas / Cell: secretory cells / Organelle: ER / Location in cell: ER
Molecular weightExperimental: 400 KDa / Theoretical: 400 KDa
Recombinant expressionOrganism: Canis lupus familiaris (dog)

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Macromolecule #2: tRNA

MacromoleculeName: tRNA / type: ligand / ID: 2 / Name.synonym: tRNA / Details: q / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Canis lupus familiaris (dog) / synonym: Dog
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa
Recombinant expressionOrganism: wheat germ (plant)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.3 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Average electron dose: 10 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider

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Atomic model buiding 1

DetailsThe domains were separately fitted by manual docking using program O
RefinementProtocol: RIGID BODY FIT
Output model

PDB-1ry1:
Structure of the signal recognition particle interacting with the elongation-arrested ribosome

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