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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 / 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
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single 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 Report
SummaryFull reportAbout validation report
DateDeposition: Nov 16, 2018 / Release: Dec 19, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 19, 2018Structure modelrepositoryInitial release
1.1Dec 26, 2018Structure modelData collection / Database referencescitation_citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
1.2Jan 16, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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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
Polyers191,9876
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/peptide Protein transport protein SEC61 / Protein targeting / Sec61 complex subunit SEC61 / Sec61 complex subunit alpha


Mass: 52978.148 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32915
#2: Protein/peptide Protein transport protein SSS1 / Protein targeting / 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35179
#3: Protein/peptide Protein transport protein SBH1 / Protein targeting / Sec61 complex subunit SBH1 / Sec61 complex subunit beta


Mass: 8723.155 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P52870

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Protein/peptide , 1 types, 1 molecules D

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


Mass: 75432.258 Da / Num. of mol.: 1
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/peptide Translocation protein SEC66 / Protein HSS1 / Sec62/63 complex 31.5 kDa subunit


Mass: 24263.939 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33754
#6: Protein/peptide Translocation protein SEC72 / Sec62/63 complex 23 kDa subunit / p23


Mass: 21631.090 Da / Num. of mol.: 1
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 / 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 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder 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
4CTFFIND4.10CTF 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 selectionNumber of particles selected: 358961
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 172531 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingPDB-ID: 5L0W

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