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- PDB-2akh: Normal mode-based flexible fitted coordinates of a non-translocat... -

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Entry
Database: PDB / ID: 2akh
TitleNormal mode-based flexible fitted coordinates of a non-translocating SecYEG protein-conducting channel into the cryo-EM map of a SecYEG-nascent chain-70S ribosome complex from E. coli
DescriptorProtein-export membrane protein secG
Preprotein translocase secY subunit
Preprotein translocase secE subunit
KeywordsPROTEIN TRANSPORT / Protein transport / Translocation / Transmembrane / Transport
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (14.9 Å resolution / Particle / Single particle)
AuthorsMitra, K.M. / Schaffitzel, C. / Shaikh, T. / Tama, F. / Jenni, S. / Brooks III, C.L. / Ban, N. / Frank, J.
CitationNature, 2005, 438, 318-324

Nature, 2005, 438, 318-324 Yorodumi Papers
Structure of the E. coli protein-conducting channel bound to a translating ribosome.
Kakoli Mitra / Christiane Schaffitzel / Tanvir Shaikh / Florence Tama / Simon Jenni / Charles L Brooks / Nenad Ban / Joachim Frank

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 3, 2005 / Release: Nov 15, 2005
RevisionDateData content typeGroupProviderType
1.0Nov 15, 2005Structure modelrepositoryInitial release
1.1Apr 30, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
X: Protein-export membrane protein secG
Y: Preprotein translocase secY subunit
Z: Preprotein translocase secE subunit
A: Protein-export membrane protein secG
B: Preprotein translocase secY subunit
C: Preprotein translocase secE subunit


Theoretical massNumber of molelcules
Total (without water)127,9266
Polyers127,9266
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)Protein-export membrane protein secG / Preprotein translocase band 1 subunit / P12 / Coordinate model: Cα atoms only


Mass: 7906.356 Da / Num. of mol.: 2
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P33582

Cellular component

Molecular function

  • P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO: 0015450)
  • protein transmembrane transporter activity (GO: 0008320)

Biological process

  • intracellular protein transmembrane transport (GO: 0065002)
  • intracellular protein transport (GO: 0006886)
  • protein insertion into membrane from inner side (GO: 0032978)
  • protein secretion (GO: 0009306)
  • protein transport by the Sec complex (GO: 0043952)
  • SRP-dependent cotranslational protein targeting to membrane, translocation (GO: 0006616)
#2: Polypeptide(L)Preprotein translocase secY subunit / Coordinate model: Cα atoms only


Mass: 43961.035 Da / Num. of mol.: 2 / Fragment: plug TMH 2a deleted / Mutation: DEL(40-75)
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P03844

Cellular component

Molecular function

Biological process

  • intracellular protein transmembrane transport (GO: 0065002)
  • intracellular protein transport (GO: 0006886)
  • protein insertion into membrane from inner side (GO: 0032978)
  • protein transport by the Sec complex (GO: 0043952)
  • SRP-dependent cotranslational protein targeting to membrane, translocation (GO: 0006616)
#3: Polypeptide(L)Preprotein translocase secE subunit / Coordinate model: Cα atoms only


Mass: 12095.701 Da / Num. of mol.: 2
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P16920

Cellular component

Molecular function

  • P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO: 0015450)
  • protein transmembrane transporter activity (GO: 0008320)

Biological process

  • intracellular protein transmembrane transport (GO: 0065002)
  • intracellular protein transport (GO: 0006886)
  • protein insertion into membrane from inner side (GO: 0032978)
  • protein secretion (GO: 0009306)
  • protein transport by the Sec complex (GO: 0043952)
  • SRP-dependent cotranslational protein targeting to membrane, translocation (GO: 0006616)

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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

Component
IDNameTypeParent IDDetails
1protein-conducting channelCOMPLEX0
2protein translocase activity1dimer of SecYEG heterotrimer
3protein translocase activity1dimer of SecYEG heterotrimer
4protein translocase activity1dimer of SecYEG heterotrimer
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 93 K / Humidity: 90 % / Method: Blot for 2 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30 / Date: Mar 9, 2004
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 / Calibrated magnification: 39000 / Nominal defocus max: 4300 nm / Nominal defocus min: 1500 nm / Cs: 2.26 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: Cryo Stage / Temperature: 93 kelvins
Image recordingElectron dose: 11 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1RSR2000MODEL FITTING
2SPIDERRECONSTRUCTION
CTF correctionDetails: defocus groups
SymmetryPoint symmetry: C1
3D reconstructionResolution: 14.9 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 53325 / Details: The resolution is based on FSC at 0.5 cut-off / Symmetry type: POINT
Atomic model buildingDetails: METHOD--normal mode-based flexible fitting REFINEMENT PROTOCOL--normal mode-based flexible fitting, real space refinement
Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: correlation coefficient, R-factor
Number of atoms included #LASTProtein: 1176 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1176

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