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- PDB-6nd1: CryoEM structure of the Sec Complex from yeast -

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Basic information

Entry
Database: PDB / ID: 6nd1
TitleCryoEM structure of the Sec Complex from yeast
Components
  • (Protein transport protein ...Protein targeting) x 3
  • (Translocation protein ...) x 2
  • Protein translocation protein SEC63Protein targeting
KeywordsPROTEIN TRANSPORT / Sec61 / post-translational translocation / yeast / Sec63 / TRANSPORT PROTEIN
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 / 4.1 Å resolution
AuthorsWu, X. / Cabanos, C. / Rapoport, T.A.
CitationJournal: Nature / Year: 2018
Title: Structure of the post-translational protein translocation machinery of the ER membrane
Authors: Wu, X. / Cabanos, C. / Rapoport, T.A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 13, 2018 / Release: Jan 9, 2019

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)193,3876
Polyers193,3876
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, All components were purified by affinity purification and subjected to gel filtration, the bands were confirmed by mass-spec
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#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: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32915
#3: 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: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P35179
#4: 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 (baker's yeast) / References: UniProt: P52870

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Protein/peptide , 1 types, 1 molecules A

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


Mass: 76831.602 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Saccharomyces cerevisiae (baker's yeast) / 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 (baker's yeast) / 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 (baker's yeast) / 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: The yeast Sec Complex involved in post-translational protein translocation
Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer ID
1150 mMsodium chlorideNaCl1
225 mMHEPESC8H18N2O4S1
30.05 %DigitoninC56H92O291
SpecimenConc.: 6 mg/ml / Details: This sample was monodisperse / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 kelvins / Details: blot for 2.5 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 54.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4GctfCTF correction
9RELION3.0initial Euler assignment
10RELION3.0final Euler assignment
13PHENIXmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 91218 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL
Least-squares processHighest resolution: 4.1 Å

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