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- PDB-6n3q: Cryo-EM structure of the yeast Sec complex -

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Basic information

Entry
Database: PDB / ID: 6n3q
TitleCryo-EM structure of the yeast Sec complex
Components
  • (Protein transport protein ...Protein targeting) x 3
  • (Translocation protein ...) x 2
  • Protein translocation protein SEC63Protein targeting
KeywordsTRANSPORT PROTEIN / Sec61 / Sec63 / Sec71 / Sec72 / Sec66 / protein translocation / translocon / endoplasmic reticulum / secretion
Function / homology
Function and homology information


Sec62/Sec63 complex / Ssh1 translocon complex / misfolded protein transport / protein transmembrane import into intracellular organelle / 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 / Ssh1 translocon complex / misfolded protein transport / protein transmembrane import into intracellular organelle / 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
Preprotein translocase subunit Sec66 / SecY domain superfamily / Sec63 domain / Protein translocase SEC61 complex, gamma subunit / Tetratricopeptide-like helical domain superfamily / Immunoglobulin E-set / Protein transport protein SecG/Sec61-beta/Sbh / DnaJ domain, conserved site / Translocation protein Sec66 / Translocon Sec61/SecY, plug domain ...Preprotein translocase subunit Sec66 / SecY domain superfamily / Sec63 domain / Protein translocase SEC61 complex, gamma subunit / Tetratricopeptide-like helical domain superfamily / Immunoglobulin E-set / Protein transport protein SecG/Sec61-beta/Sbh / DnaJ domain, conserved site / Translocation protein Sec66 / Translocon Sec61/SecY, plug domain / Tetratricopeptide repeat / Protein translocase SecE domain superfamily / DnaJ domain / Translocation protein Sec63 / SecY conserved site / Protein transport Sec61-beta/Sbh / Chaperone J-domain superfamily / SecY translocase / Plug domain of Sec61p / Sec61beta family / SecE/Sec61-gamma subunits of protein translocation complex / DnaJ domain / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family
Protein transport protein SBH1 / Translocation protein SEC72 / Translocation protein SEC66 / Protein transport protein SEC61 / Protein translocation protein SEC63 / Protein transport protein SSS1
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å
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 Report
SummaryFull reportAbout validation report
History
DepositionNov 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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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


Theoretical massNumber of molelcules
Total (without water)191,9876
Polymers191,9876
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein transport protein ... , 3 types, 3 molecules ACB

#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 (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P52870

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Protein , 1 types, 1 molecules D

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


Mass: 75432.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14906

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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 (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39742

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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: Posttranslational Sec protein-translocation channel complex
Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
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

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 43103 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
7Coot0.8.9.1model fitting
9cryoSPARC2.0.27initial Euler assignment
10cryoSPARC2.0.27final Euler assignment
11cryoSPARC2.0.27classification
12cryoSPARC2.0.273D reconstruction
13PHENIX1.14model refinementreal space refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 358961
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172531 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingPDB-ID: 5L0W

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