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- PDB-4cg6: Cryo-em of the Sec61-complex bound to the 80s ribosome translatin... -

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Entry
Database: PDB / ID: 4cg6
TitleCryo-em of the Sec61-complex bound to the 80s ribosome translating a membrane-inserting substrate
DescriptorPEPTIDE
(PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ...) x 3
KeywordsPROTEIN TRANSPORT / CO-TRANSLATIONAL PROTEIN TRANSLOCATION
Specimen sourceCanis lupus familiaris / mammal / DOG /
MethodElectron microscopy (7.8 Å resolution / Particle / Single particle)
AuthorsGogala, M. / Becker, T. / Beatrix, B. / Barrio-Garcia, C. / Berninghausen, O. / Beckmann, R.
CitationNature, 2014, 506, 107-110

Nature, 2014, 506, 107-110 StrPapers
Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion.
Marko Gogala / Thomas Becker / Birgitta Beatrix / Jean-Paul Armache / Clara Barrio-Garcia / Otto Berninghausen / Roland Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 21, 2013 / Release: Feb 5, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 5, 2014Structure modelrepositoryInitial release
1.1Feb 12, 2014Structure modelDatabase references
1.2Feb 19, 2014Structure modelDatabase references
1.3Aug 30, 2017Structure modelData collectionem_software_em_software.fitting_id / _em_software.image_processing_id

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Assembly

Deposited unit
A: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1
B: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA
C: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA
D: PEPTIDE


Theoretical massNumber of molelcules
Total (without water)71,8584
Polyers71,8584
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Polypeptide(L)PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1 / SEC61 ALPHA-1


Mass: 52279.379 Da / Num. of mol.: 1 / Details: DATA-SUBSET RESULTED FROM COMPUTATIONAL SORTING / Source: (natural) Canis lupus familiaris / mammal / / References: UniProt: P38377

Cellular component

  • endoplasmic reticulum membrane (GO: 0005789)
  • integral component of endoplasmic reticulum membrane (GO: 0030176)

Biological process

#2: Polypeptide(L)PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA


Mass: 7752.325 Da / Num. of mol.: 1 / Details: DATA-SUBSET RESULTED FROM COMPUTATIONAL SORTING / Source: (natural) Canis lupus familiaris / mammal / / References: UniProt: P60058

Cellular component

  • endoplasmic reticulum membrane (GO: 0005789)
  • integral component of endoplasmic reticulum membrane (GO: 0030176)

Molecular function

Biological process

#3: Polypeptide(L)PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA


Mass: 9987.456 Da / Num. of mol.: 1 / Details: DATA-SUBSET RESULTED FROM COMPUTATIONAL SORTING / Source: (natural) Canis lupus familiaris / mammal / / References: UniProt: P60467

Cellular component

Molecular function

Biological process

  • posttranslational protein targeting to membrane, translocation (GO: 0031204)
  • protein import into nucleus, translocation (GO: 0000060)
  • retrograde protein transport, ER to cytosol (GO: 0030970)
  • SRP-dependent cotranslational protein targeting to membrane, translocation (GO: 0006616)
  • ubiquitin-dependent ERAD pathway (GO: 0030433)
#4: Polypeptide(L)PEPTIDE


Mass: 1839.265 Da / Num. of mol.: 1 / Details: DATA-SUBSET RESULTED FROM COMPUTATIONAL SORTING / Source: (natural) Canis lupus familiaris / mammal /

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: CANIS FAMILIARIS SEC61 BOUND TO A WHEAT GERM 80S-RNC TRANSLATING THE MEMBRANE- INSERTING LEPM-POLYPEPTIDE
Type: RIBOSOME
Buffer solutionName: 30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT
Details: 30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT
pH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Jul 17, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 148721 / Nominal defocus max: 4000 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
Image scansNumber digital images: 9805
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryImage processing IDFitting ID
1MAPPOSCLASSIFICATION1
2CootMODEL FITTING1
3MDFFMODEL FITTING1
4UCSF ChimeraMODEL FITTING1
5SignaturePARTICLE SELECTION1
6SPIDERRECONSTRUCTION1
CTF correctionDetails: ON 3D-VOLUME (SPIDER)
SymmetryPoint symmetry: C1
3D reconstructionResolution: 7.8 Å / Number of particles: 30455
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2512 (DEPOSITION ID: 12127).
Symmetry type: POINT
Atomic model buildingDetails: METHOD--FLEXIBLE / Ref protocol: FLEXIBLE FIT / Ref space: REAL
Atomic model buildingPDB-ID: 2WWB
Least-squares processHighest resolution: 7.8 Å
Refine hist #LASTHighest resolution: 7.8 Å
Number of atoms included #LASTProtein: 4383 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 4383

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