[English] 日本語
Yorodumi
- PDB-7kai: Cryo-EM structure of the Sec complex from S. cerevisiae, wild-typ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kai
TitleCryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with Sec62, conformation 1 (C1)
Components
  • (Protein transport protein ...Protein targeting) x 4
  • (Translocation protein ...) x 2
  • Protein translocation protein SEC63Protein targeting
KeywordsPROTEIN TRANSPORT / Sec61 / translocon / endoplasmic reticulum / protein translocation / Sec62 / Sec63 / channel
Function / homology
Function and homology information


protein transmembrane import into intracellular organelle / misfolded protein transport / Sec62/Sec63 complex / translocon complex / cytosol to endoplasmic reticulum transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / rough endoplasmic reticulum membrane / Ssh1 translocon complex / Sec61 translocon complex / protein-transporting ATPase activity ...protein transmembrane import into intracellular organelle / misfolded protein transport / Sec62/Sec63 complex / translocon complex / cytosol to endoplasmic reticulum transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / rough endoplasmic reticulum membrane / Ssh1 translocon complex / Sec61 translocon complex / protein-transporting ATPase activity / post-translational protein targeting to endoplasmic reticulum membrane / filamentous growth / SRP-dependent cotranslational protein targeting to membrane, translocation / peptide transmembrane transporter activity / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane / post-translational protein targeting to membrane, translocation / nuclear inner membrane / retrograde protein transport, ER to cytosol / protein transmembrane transporter activity / : / guanyl-nucleotide exchange factor activity / cell periphery / ribosome binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / mitochondrion / membrane / cytosol
Similarity search - Function
Translocation protein Sec66 / Preprotein translocase subunit Sec66 / 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 / Nt-dnaJ domain signature. ...Translocation protein Sec66 / Preprotein translocase subunit Sec66 / 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 / Nt-dnaJ domain signature. / DnaJ domain, conserved site / 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 / Sec63 domain / Sec63 Brl domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Protein translocation protein SEC63 / Protein transport protein SEC61 / Translocation protein SEC66 / Protein transport protein SSS1 / Translocation protein SEC72 / Protein transport protein SBH1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae BY4741 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsItskanov, S. / Park, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62.
Authors: Samuel Itskanov / Katie M Kuo / James C Gumbart / Eunyong Park /
Abstract: Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional proteins, Sec62 and Sec63, but their ...Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional proteins, Sec62 and Sec63, but their functions are poorly defined. In the present study, we determined cryo-electron microscopy (cryo-EM) structures of several variants of Sec61-Sec62-Sec63 complexes from Saccharomyces cerevisiae and Thermomyces lanuginosus and show that Sec62 and Sec63 induce opening of the Sec61 channel. Without Sec62, the translocation pore of Sec61 remains closed by the plug domain, rendering the channel inactive. We further show that the lateral gate of Sec61 must first be partially opened by interactions between Sec61 and Sec63 in cytosolic and luminal domains, a simultaneous disruption of which completely closes the channel. The structures and molecular dynamics simulations suggest that Sec62 may also prevent lipids from invading the channel through the open lateral gate. Our study shows how Sec63 and Sec62 work together in a hierarchical manner to activate Sec61 for post-translational protein translocation.
History
DepositionOct 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-22771
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein transport protein SEC61
C: Protein transport protein SSS1
B: Protein transport protein SBH1
D: Protein translocation protein SEC63
E: Translocation protein SEC66
F: Translocation protein SEC72
G: Protein transport protein Sec62


Theoretical massNumber of molelcules
Total (without water)199,2737
Polymers199,2737
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18690 Å2
ΔGint-159 kcal/mol
Surface area71960 Å2

-
Components

-
Protein transport protein ... , 4 types, 4 molecules ACBG

#1: Protein Protein transport protein SEC61 / Protein targeting / Sec61 complex subunit SEC61 / Sec61 complex subunit alpha


Mass: 52978.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Plasmid details: SEC63 is chromosomally tagged with TEV-GFP / Strain: ATCC 204508 / S288c / References: UniProt: P32915
#2: Protein Protein transport protein SSS1 / Protein targeting / Sec61 complex subunit SSS1 / Sec61 complex subunit gamma / Ssh1 complex subunit SSS1 / Ssh1 complex ...Sec61 complex subunit SSS1 / Sec61 complex subunit gamma / Ssh1 complex subunit SSS1 / Ssh1 complex subunit gamma


Mass: 8958.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Plasmid details: SEC63 is chromosomally tagged with TEV-GFP / Strain: ATCC 204508 / S288c / References: UniProt: P35179
#3: Protein Protein transport protein SBH1 / Protein targeting / Sec61 complex subunit SBH1 / Sec61 complex subunit beta


Mass: 8723.155 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Plasmid details: SEC63 is chromosomally tagged with TEV-GFP / Strain: ATCC 204508 / S288c / References: UniProt: P52870
#7: Protein Protein transport protein Sec62 / Protein targeting


Mass: 4783.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Plasmid details: SEC63 is chromosomally tagged with TEV-GFP / Strain: ATCC 204508 / S288c

-
Protein , 1 types, 1 molecules D

#4: Protein Protein translocation protein SEC63 / Protein targeting / Protein NPL1 / Sec62/63 complex 73 kDa subunit


Mass: 77933.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae BY4741 (yeast)
Strain: ATCC 204508 / S288c / Production host: Saccharomyces cerevisiae BY4741 (yeast) / Strain (production host): ATCC 204508 / S288c / References: UniProt: P14906

-
Translocation protein ... , 2 types, 2 molecules EF

#5: Protein Translocation protein SEC66 / Protein HSS1 / Sec62/63 complex 31.5 kDa subunit


Mass: 24263.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Plasmid details: SEC63 is chromosomally tagged with TEV-GFP / Strain: ATCC 204508 / S288c / References: UniProt: P33754
#6: Protein Translocation protein SEC72 / Sec62/63 complex 23 kDa subunit / p23


Mass: 21631.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / Plasmid details: SEC63 is chromosomally tagged with TEV-GFP / Strain: ATCC 204508 / S288c / References: UniProt: P39742

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Endoplasmic reticulum protein-transport machinery Sec complex from yeast
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast) / Strain: ATCC 204508 / S288c
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 42017 X / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

-
Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
1Warp1.0.7particle selection
2SerialEM3.7image acquisition
4Warp1.0.7CTF correction
5cryoSPARC2.12CTF correction
11cryoSPARC2.12initial Euler assignment
12cryoSPARC2.12final Euler assignment
14cryoSPARC2.123D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2686839 / Details: autopicked particles
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193263 / Algorithm: FOURIER SPACE / Details: Non-uniform refinement from cryoSPARC / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310924
ELECTRON MICROSCOPYf_angle_d0.49914819
ELECTRON MICROSCOPYf_dihedral_angle_d11.056579
ELECTRON MICROSCOPYf_chiral_restr0.0381769
ELECTRON MICROSCOPYf_plane_restr0.0041850

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more