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

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Basic information

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
Components
  • Preprotein translocase secE subunit
  • Preprotein translocase secY subunit
  • Protein-export membrane protein secG
KeywordsPROTEIN TRANSPORT / Protein transport / Translocation / Transmembrane / Transport
Function / homologyPreprotein translocase SecG subunit / SecE superfamily / Protein translocase complex, SecE/Sec61-gamma subunit / Preprotein translocase subunit SecE / SecY domain superfamily / Protein translocase subunit SecY / SecE subunit of protein translocation complex / SecY conserved site / SecY translocase / SecE/Sec61-gamma subunits of protein translocation complex ...Preprotein translocase SecG subunit / SecE superfamily / Protein translocase complex, SecE/Sec61-gamma subunit / Preprotein translocase subunit SecE / SecY domain superfamily / Protein translocase subunit SecY / SecE subunit of protein translocation complex / SecY conserved site / SecY translocase / SecE/Sec61-gamma subunits of protein translocation complex / Preprotein translocase SecG subunit / Protein secY signature 1. / Protein secY signature 2. / Protein secE/sec61-gamma signature. / SecY/SEC61-alpha family / protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / signal sequence binding / intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / P-P-bond-hydrolysis-driven protein transmembrane transporter activity / protein targeting / protein transmembrane transporter activity / protein secretion / intracellular protein transport / protein transport / intracellular / integral component of plasma membrane / integral component of membrane / plasma membrane / Protein translocase subunit SecY / Protein translocase subunit SecE / Protein-export membrane protein SecG / Protein translocase subunit SecY / Protein translocase subunit SecE / Protein-export membrane protein SecG
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 14.9 Å resolution
AuthorsMitra, K.M. / Schaffitzel, C. / Shaikh, T. / Tama, F. / Jenni, S. / Brooks III, C.L. / Ban, N. / Frank, J.
CitationJournal: Nature / Year: 2005
Title: Structure of the E. coli protein-conducting channel bound to a translating ribosome.
Authors: 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: Protein/peptide 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 (E. coli) / Genus: Escherichia / Gene: secG / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P33582, UniProt: P0AG99*PLUS
#2: Protein/peptide 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 (E. coli) / Genus: Escherichia / Gene: secY, prlA / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P03844, UniProt: P0AGA2*PLUS
#3: Protein/peptide Preprotein translocase secE subunit / Coordinate model: Cα atoms only


Mass: 12095.701 Da / Num. of mol.: 2 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Gene: secE, prlG / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P16920, UniProt: P0AG96*PLUS

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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

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 FIELDBright-field microscopy / 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
2SPIDER3D reconstruction
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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