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- PDB-2aki: Normal mode-based flexible fitted coordinates of a translocating ... -

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Entry
Database: PDB / ID: 2aki
TitleNormal mode-based flexible fitted coordinates of a 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 / Translocation / Transmembrane / Transport
Function / homology
Function and homology information


protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting ...protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting / membrane => GO:0016020 / intracellular protein transport / membrane / plasma membrane
Similarity search - Function
Preprotein translocase SecG subunit / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit ...Preprotein translocase SecG subunit / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY
Similarity search - Domain/homology
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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14.9 Å
AuthorsMitra, K. / 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 /
Abstract: Secreted and membrane proteins are translocated across or into cell membranes through a protein-conducting channel (PCC). Here we present a cryo-electron microscopy reconstruction of the Escherichia ...Secreted and membrane proteins are translocated across or into cell membranes through a protein-conducting channel (PCC). Here we present a cryo-electron microscopy reconstruction of the Escherichia coli PCC, SecYEG, complexed with the ribosome and a nascent chain containing a signal anchor. This reconstruction shows a messenger RNA, three transfer RNAs, the nascent chain, and detailed features of both a translocating PCC and a second, non-translocating PCC bound to mRNA hairpins. The translocating PCC forms connections with ribosomal RNA hairpins on two sides and ribosomal proteins at the back, leaving a frontal opening. Normal mode-based flexible fitting of the archaeal SecYEbeta structure into the PCC electron microscopy densities favours a front-to-front arrangement of two SecYEG complexes in the PCC, and supports channel formation by the opening of two linked SecY halves during polypeptide translocation. On the basis of our observation in the translocating PCC of two segregated pores with different degrees of access to bulk lipid, we propose a model for co-translational protein translocation.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Polymers127,9266
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein 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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: secG / Production host: Escherichia coli (E. coli) / References: UniProt: P33582, UniProt: P0AG99*PLUS
#2: Protein Preprotein translocase secY subunit / Coordinate model: Cα atoms only


Mass: 43961.035 Da / Num. of mol.: 2 / Fragment: plug TMH 2a omitted / Mutation: DEL (40-75)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: secY, prlA / Production host: Escherichia coli (E. coli) / References: UniProt: P03844, UniProt: P0AGA2*PLUS
#3: Protein Preprotein translocase secE subunit / Coordinate model: Cα atoms only


Mass: 12095.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: secE, prlG / 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 / 3D 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

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: 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 X / Calibrated magnification: 39000 X / 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 K
Image recordingElectron dose: 11 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (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 (asymmetric)
3D reconstructionResolution: 14.9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 53325 / Details: The resolution is based on FSC at 0.5 cut-off / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation coefficient, R-factor
Details: METHOD--normal mode-based flexible fitting REFINEMENT PROTOCOL--normal mode-based flexible fitting, real space refinement
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 0 0 1176

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