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- PDB-4cg6: Cryo-em of the Sec61-complex bound to the 80s ribosome translatin... -

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Basic information

Entry
Database: PDB / ID: 4cg6
TitleCryo-em of the Sec61-complex bound to the 80s ribosome translating a membrane-inserting substrate
Components
  • PEPTIDE
  • PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1
  • PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA
  • PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA
KeywordsPROTEIN TRANSPORT / CO-TRANSLATIONAL PROTEIN TRANSLOCATION
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / endoplasmic reticulum Sec complex / pronephric nephron development / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein insertion into ER membrane / protein-transporting ATPase activity ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / endoplasmic reticulum Sec complex / pronephric nephron development / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein insertion into ER membrane / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / post-translational protein targeting to membrane, translocation / protein transmembrane transporter activity / guanyl-nucleotide exchange factor activity / phospholipid binding / ribosome binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. ...Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY
Similarity search - Domain/homology
Protein transport protein Sec61 subunit alpha isoform 1 / Protein transport protein Sec61 subunit gamma / Protein transport protein Sec61 subunit beta
Similarity search - Component
Biological speciesCANIS LUPUS FAMILIARIS (dog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsGogala, M. / Becker, T. / Beatrix, B. / Barrio-Garcia, C. / Berninghausen, O. / Beckmann, R.
CitationJournal: Nature / Year: 2014
Title: Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion.
Authors: Marko Gogala / Thomas Becker / Birgitta Beatrix / Jean-Paul Armache / Clara Barrio-Garcia / Otto Berninghausen / Roland Beckmann /
Abstract: The biogenesis of secretory as well as transmembrane proteins requires the activity of the universally conserved protein-conducting channel (PCC), the Sec61 complex (SecY complex in bacteria). In ...The biogenesis of secretory as well as transmembrane proteins requires the activity of the universally conserved protein-conducting channel (PCC), the Sec61 complex (SecY complex in bacteria). In eukaryotic cells the PCC is located in the membrane of the endoplasmic reticulum where it can bind to translating ribosomes for co-translational protein transport. The Sec complex consists of three subunits (Sec61α, β and γ) and provides an aqueous environment for the translocation of hydrophilic peptides as well as a lateral opening in the Sec61α subunit that has been proposed to act as a gate for the membrane partitioning of hydrophobic domains. A plug helix and a so-called pore ring are believed to seal the PCC against ion flow and are proposed to rearrange for accommodation of translocating peptides. Several crystal and cryo-electron microscopy structures revealed different conformations of closed and partially open Sec61 and SecY complexes. However, in none of these samples has the translocation state been unambiguously defined biochemically. Here we present cryo-electron microscopy structures of ribosome-bound Sec61 complexes engaged in translocation or membrane insertion of nascent peptides. Our data show that a hydrophilic peptide can translocate through the Sec complex with an essentially closed lateral gate and an only slightly rearranged central channel. Membrane insertion of a hydrophobic domain seems to occur with the Sec complex opening the proposed lateral gate while rearranging the plug to maintain an ion permeability barrier. Taken together, we provide a structural model for the basic activities of the Sec61 complex as a protein-conducting channel.
History
DepositionNov 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.4May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1
B: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA
C: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA
D: PEPTIDE


Theoretical massNumber of molelcules
Total (without water)71,8584
Polymers71,8584
Non-polymers00
Water00
1


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

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Components

#1: Protein PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1 / SEC61 ALPHA-1


Mass: 52279.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DATA-SUBSET RESULTED FROM COMPUTATIONAL SORTING / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / Organ: PANCREAS / References: UniProt: P38377
#2: Protein PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA


Mass: 7752.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DATA-SUBSET RESULTED FROM COMPUTATIONAL SORTING / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / Organ: PANCREAS / References: UniProt: P60058
#3: Protein PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA


Mass: 9987.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DATA-SUBSET RESULTED FROM COMPUTATIONAL SORTING / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / Organ: PANCREAS / References: UniProt: P60467
#4: Protein/peptide PEPTIDE


Mass: 1839.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DATA-SUBSET RESULTED FROM COMPUTATIONAL SORTING / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / Organ: PANCREAS

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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: CANIS FAMILIARIS SEC61 BOUND TO A WHEAT GERM 80S-RNC TRANSLATING THE MEMBRANE- INSERTING LEPM-POLYPEPTIDE
Type: RIBOSOME
Buffer solutionName: 30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT
pH: 7.6
Details: 30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 17, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 148721 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
Image scansNum. digital images: 9805
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1MAPPOSclassification
2Cootmodel fitting
3MDFFmodel fitting
4UCSF Chimeramodel fitting
5Signatureparticle selection
6SPIDER3D reconstruction
CTF correctionDetails: ON 3D-VOLUME (SPIDER)
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.8 Å / Num. of particles: 30455
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2512 (DEPOSITION ID: 12127).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--FLEXIBLE
Atomic model buildingPDB-ID: 2WWB

2wwb


Accession code: 2WWB / Source name: PDB / Type: experimental model
RefinementHighest resolution: 7.8 Å
Refinement stepCycle: LAST / Highest resolution: 7.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 0 0 4383

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