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- EMDB-0336: Cryo-EM structure of the yeast Sec complex -

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Basic information

Entry
Database: EMDB / ID: 0336
TitleCryo-EM structure of the yeast Sec complex
Map dataSharpened full map
SamplePosttranslational Sec protein-translocation channel complex
  • (Protein transport protein ...Protein targeting) x 3
  • Protein translocation protein SEC63Protein targeting
  • (Translocation protein ...) x 2
Function / homologyTetratricopeptide-like helical domain superfamily / Protein transport protein SecG/Sec61-beta/Sbh / DnaJ domain / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / Sec63 domain / Protein translocase SEC61 complex, gamma subunit / Immunoglobulin E-set / DnaJ domain, conserved site / Chaperone J-domain superfamily ...Tetratricopeptide-like helical domain superfamily / Protein transport protein SecG/Sec61-beta/Sbh / DnaJ domain / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / Sec63 domain / Protein translocase SEC61 complex, gamma subunit / Immunoglobulin E-set / DnaJ domain, conserved site / Chaperone J-domain superfamily / Translocation protein Sec66 / Translocon Sec61/SecY, plug domain / Tetratricopeptide repeat / SecY domain superfamily / Protein translocase SecE domain superfamily / Translocation protein Sec63 / SecY conserved site / DnaJ domain / Protein transport Sec61-beta/Sbh / Protein secY signature 1. / XBP1(S) activates chaperone genes / SecY translocase / dnaJ domain profile. / SecE/Sec61-gamma subunits of protein translocation complex / Sec61beta family / Preprotein translocase subunit Sec66 / Protein secE/sec61-gamma signature. / Plug domain of Sec61p / Nt-dnaJ domain signature. / Protein secY signature 2. / Sec62/Sec63 complex / cytosol to endoplasmic reticulum transport / misfolded protein transport / protein transmembrane import into intracellular organelle / Ssh1 translocon complex / endoplasmic reticulum Sec complex / Sec61 translocon complex / posttranslational protein targeting to membrane, translocation / filamentous growth / posttranslational protein targeting to endoplasmic reticulum membrane / ARF guanyl-nucleotide exchange factor activity / P-P-bond-hydrolysis-driven protein transmembrane transporter activity / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / retrograde protein transport, ER to cytosol / nuclear inner membrane / peptide transmembrane transporter activity / integral component of endoplasmic reticulum membrane / protein transmembrane transporter activity / SRP-dependent cotranslational protein targeting to membrane / ubiquitin-dependent ERAD pathway / protein transporter activity / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / integral component of membrane / Protein translocation protein SEC63 / Protein transport protein SEC61 / Translocation protein SEC66 / Protein transport protein SSS1 / Translocation protein SEC72 / Protein transport protein SBH1
Function and homology information
SourceSaccharomyces cerevisiae S288c (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 3.68 Å resolution
AuthorsPark E / Itskanov S
CitationJournal: Science / Year: 2019
Title: Structure of the posttranslational Sec protein-translocation channel complex from yeast.
Authors: Samuel Itskanov / Eunyong Park
Abstract: The Sec61 protein-conducting channel mediates transport of many proteins, such as secretory proteins, across the endoplasmic reticulum (ER) membrane during or after translation. Posttranslational ...The Sec61 protein-conducting channel mediates transport of many proteins, such as secretory proteins, across the endoplasmic reticulum (ER) membrane during or after translation. Posttranslational transport is enabled by two additional membrane proteins associated with the channel, Sec63 and Sec62, but its mechanism is poorly understood. We determined a structure of the Sec complex (Sec61-Sec63-Sec71-Sec72) from by cryo-electron microscopy (cryo-EM). The structure shows that Sec63 tightly associates with Sec61 through interactions in cytosolic, transmembrane, and ER-luminal domains, prying open Sec61's lateral gate and translocation pore and thus activating the channel for substrate engagement. Furthermore, Sec63 optimally positions binding sites for cytosolic and luminal chaperones in the complex to enable efficient polypeptide translocation. Our study provides mechanistic insights into eukaryotic posttranslational protein translocation.
Validation ReportPDB-ID: 6n3q

SummaryFull reportAbout validation report
DateDeposition: Nov 16, 2018 / Header (metadata) release: Dec 12, 2018 / Map release: Dec 19, 2018 / Last update: Dec 26, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.42
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.42
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6n3q
  • Surface level: 0.42
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0336.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.16 Å/pix.
= 296.96 Å
256 pix
1.16 Å/pix.
= 296.96 Å
256 pix
1.16 Å/pix.
= 296.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density
Contour Level:0.42 (by author), 0.42 (movie #1):
Minimum - Maximum-1.1991107 - 3.022722
Average (Standard dev.)0.009868922 (0.06600453)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 296.96 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z296.960296.960296.960
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.1993.0230.010

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Supplemental data

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Sample components

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Entire Posttranslational Sec protein-translocation channel complex

EntireName: Posttranslational Sec protein-translocation channel complex
Number of components: 7

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Component #1: protein, Posttranslational Sec protein-translocation channel complex

ProteinName: Posttranslational Sec protein-translocation channel complex
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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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: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #3: protein, Protein transport protein SSS1

ProteinName: Protein transport protein SSS1Protein targeting / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.958641 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #4: 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) / Strain: ATCC 204508 / S288c

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Component #5: protein, Protein translocation protein SEC63

ProteinName: Protein translocation protein SEC63Protein targeting / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 75.432258 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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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) / Strain: ATCC 204508 / S288c

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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) / Strain: ATCC 204508 / S288c

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 43103.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 2400.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 172531
3D reconstructionAlgorithm: FOURIER SPACE / Software: cryoSPARC / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Input PDB model: 5L0W
Output model

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