[English] 日本語
Yorodumi
- EMDB-0440: CryoEM structure of the post-translational protein translocation ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0440
TitleCryoEM structure of the post-translational protein translocation machinery of the ER membrane
Map data
SampleThe yeast Sec Complex involved in post-translational protein translocation
  • (Protein transport protein ...Protein targeting) x 3
  • Protein translocation protein SEC63Protein targeting
  • (Translocation protein ...) x 2
Function / homology
Function and homology information


Sec62/Sec63 complex / protein transmembrane import into intracellular organelle / misfolded protein transport / Ssh1 translocon complex / cytosol to endoplasmic reticulum transport / endoplasmic reticulum Sec complex / Sec61 translocon complex / posttranslational protein targeting to membrane, translocation / posttranslational protein targeting to endoplasmic reticulum membrane / filamentous growth ...Sec62/Sec63 complex / protein transmembrane import into intracellular organelle / misfolded protein transport / Ssh1 translocon complex / cytosol to endoplasmic reticulum transport / endoplasmic reticulum Sec complex / Sec61 translocon complex / posttranslational protein targeting to membrane, translocation / posttranslational protein targeting to endoplasmic reticulum membrane / filamentous growth / SRP-dependent cotranslational protein targeting to membrane, translocation / ARF guanyl-nucleotide exchange factor activity / P-P-bond-hydrolysis-driven protein transmembrane transporter activity / signal sequence binding / retrograde protein transport, ER to cytosol / nuclear inner membrane / peptide transmembrane transporter activity / protein transmembrane transporter activity / SRP-dependent cotranslational protein targeting to membrane / ubiquitin-dependent ERAD pathway / cell periphery / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / mitochondrion / integral component of membrane
Protein transport protein SecG/Sec61-beta/Sbh / Protein translocase SEC61 complex, gamma subunit / DnaJ domain, conserved site / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / Translocon Sec61/SecY, plug domain / Tetratricopeptide repeat / DnaJ domain / SecY domain superfamily / Sec63 domain ...Protein transport protein SecG/Sec61-beta/Sbh / Protein translocase SEC61 complex, gamma subunit / DnaJ domain, conserved site / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / Translocon Sec61/SecY, plug domain / Tetratricopeptide repeat / DnaJ domain / SecY domain superfamily / Sec63 domain / Tetratricopeptide-like helical domain superfamily / Protein translocase SecE domain superfamily / Translocation protein Sec63 / SecY conserved site / Protein transport Sec61-beta/Sbh / Immunoglobulin E-set / Chaperone J-domain superfamily / Translocation protein Sec66
Protein translocation protein SEC63 / Protein transport protein SEC61 / Translocation protein SEC66 / Protein transport protein SSS1 / Translocation protein SEC72 / Protein transport protein SBH1
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWu X / Cabanos C / Rapoport TA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM052586 United States
CitationJournal: Nature / Year: 2019
Title: Structure of the post-translational protein translocation machinery of the ER membrane.
Authors: Xudong Wu / Cerrone Cabanos / Tom A Rapoport /
Abstract: Many proteins must translocate through the protein-conducting Sec61 channel in the eukaryotic endoplasmic reticulum membrane or the SecY channel in the prokaryotic plasma membrane. Proteins with ...Many proteins must translocate through the protein-conducting Sec61 channel in the eukaryotic endoplasmic reticulum membrane or the SecY channel in the prokaryotic plasma membrane. Proteins with highly hydrophobic signal sequences are first recognized by the signal recognition particle (SRP) and then moved co-translationally through the Sec61 or SecY channel by the associated translating ribosome. Substrates with less hydrophobic signal sequences bypass the SRP and are moved through the channel post-translationally. In eukaryotic cells, post-translational translocation is mediated by the association of the Sec61 channel with another membrane protein complex, the Sec62-Sec63 complex, and substrates are moved through the channel by the luminal BiP ATPase. How the Sec62-Sec63 complex activates the Sec61 channel for post-translational translocation is not known. Here we report the electron cryo-microscopy structure of the Sec complex from Saccharomyces cerevisiae, consisting of the Sec61 channel and the Sec62, Sec63, Sec71 and Sec72 proteins. Sec63 causes wide opening of the lateral gate of the Sec61 channel, priming it for the passage of low-hydrophobicity signal sequences into the lipid phase, without displacing the channel's plug domain. Lateral channel opening is triggered by Sec63 interacting both with cytosolic loops in the C-terminal half of Sec61 and transmembrane segments in the N-terminal half of the Sec61 channel. The cytosolic Brl domain of Sec63 blocks ribosome binding to the channel and recruits Sec71 and Sec72, positioning them for the capture of polypeptides associated with cytosolic Hsp70. Our structure shows how the Sec61 channel is activated for post-translational protein translocation.
History
DepositionDec 13, 2018-
Header (metadata) releaseJan 9, 2019-
Map releaseJan 9, 2019-
UpdateJan 8, 2020-
Current statusJan 8, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6nd1
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_0440.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 160 pix.
= 216. Å
1.35 Å/pix.
x 160 pix.
= 216. Å
1.35 Å/pix.
x 160 pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.035
Minimum - Maximum-0.13241692 - 0.19763649
Average (Standard dev.)0.00003726553 (±0.008323493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 216.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z216.000216.000216.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1320.1980.000

-
Supplemental data

-
Additional map: EM map before focused refinement, without sharpening

Fileemd_0440_additional.map
AnnotationEM map before focused refinement, without sharpening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire The yeast Sec Complex involved in post-translational protein tran...

EntireName: The yeast Sec Complex involved in post-translational protein translocation
Number of components: 7

+
Component #1: protein, The yeast Sec Complex involved in post-translational pro...

ProteinName: The yeast Sec Complex involved in post-translational protein translocation
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #2: protein, Protein transport protein SEC61

ProteinName: Protein transport protein SEC61Protein targeting / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.978148 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

+
Component #3: protein, Protein translocation protein SEC63

ProteinName: Protein translocation protein SEC63Protein targeting / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 76.831602 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

+
Component #4: protein, Protein transport protein SSS1

ProteinName: Protein transport protein SSS1Protein targeting / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.958641 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

+
Component #5: protein, Protein transport protein SBH1

ProteinName: Protein transport protein SBH1Protein targeting / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.723155 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #6: protein, Translocation protein SEC66

ProteinName: Translocation protein SEC66 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.263939 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #7: protein, Translocation protein SEC72

ProteinName: Translocation protein SEC72 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.63109 kDa
SourceSpecies: Baker's yeast (baker's yeast)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 6 mg/mL / pH: 7.4
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 90 % / Details: blot for 2.5 seconds before plunging.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 54.8 e/Å2 / Illumination mode: OTHER
LensImaging mode: OTHER
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 91218
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.:Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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