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- PDB-5mg3: EM fitted model of bacterial holo-translocon -

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Basic information

Entry
Database: PDB / ID: 5mg3
TitleEM fitted model of bacterial holo-translocon
Components
  • (Protein translocase subunit ...) x 4
  • Membrane protein insertase YidC
  • Protein-export membrane protein SecG
KeywordsCHAPERONE / holotranslocon / membrane protein insertion machinery / protein secretion
Function / homology
Function and homology information


protein insertion into membrane from inner side / membrane insertase activity / 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 insertion into membrane / protein transmembrane transporter activity ...protein insertion into membrane from inner side / membrane insertase activity / 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 insertion into membrane / protein transmembrane transporter activity / protein secretion / protein targeting / intracellular protein transport / protein transport / protein folding / protein-containing complex assembly / membrane / plasma membrane
Similarity search - Function
SecD export protein N-terminal TM domain / SecD export protein N-terminal TM region / Protein-export membrane protein SecF, bacterial / Protein translocase subunit SecD / Protein-export membrane protein SecD/SecF, bacterial / Protein-export membrane protein SecD/SecF/SecDF, conserved site / Protein-export membrane protein SecD/SecF, archaeal and bacterial / : / : / : ...SecD export protein N-terminal TM domain / SecD export protein N-terminal TM region / Protein-export membrane protein SecF, bacterial / Protein translocase subunit SecD / Protein-export membrane protein SecD/SecF, bacterial / Protein-export membrane protein SecD/SecF/SecDF, conserved site / Protein-export membrane protein SecD/SecF, archaeal and bacterial / : / : / : / Protein export membrane protein / SecD/SecF GG Motif / Protein translocase subunit SecDF, P1 domain, N-terminal / SecDF, P1 head subdomain / Membrane insertase YidC, N-terminal / YidC, periplasmic domain superfamily / YidC periplasmic domain / Membrane insertase YidC / : / Preprotein translocase SecG subunit / Preprotein translocase SecG subunit / Membrane insertase YidC/Oxa1, C-terminal / 60Kd inner membrane protein / Membrane insertase YidC/ALB3/OXA1/COX18 / 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 SecD / Protein translocase subunit SecF / Protein translocase subunit SecE / Protein-export membrane protein SecG / Protein translocase subunit SecY / Membrane protein insertase YidC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14 Å
AuthorsSchaffitzel, C. / Botte, M.
Funding support Germany, France, United Kingdom, 3items
OrganizationGrant numberCountry
Baden-Wurttemberg StiftungMeth-P-LS-4 Germany
French National Research AgencyANR- 09-JCJC-0044 France
Biotechnology and Biological Sciences Research CouncilBB/P000940/1 United Kingdom
CitationJournal: Sci Rep / Year: 2016
Title: A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion.
Authors: Mathieu Botte / Nathan R Zaccai / Jelger Lycklama À Nijeholt / Remy Martin / Kèvin Knoops / Gabor Papai / Juan Zou / Aurélien Deniaud / Manikandan Karuppasamy / Qiyang Jiang / Abhishek ...Authors: Mathieu Botte / Nathan R Zaccai / Jelger Lycklama À Nijeholt / Remy Martin / Kèvin Knoops / Gabor Papai / Juan Zou / Aurélien Deniaud / Manikandan Karuppasamy / Qiyang Jiang / Abhishek Singha Roy / Klaus Schulten / Patrick Schultz / Juri Rappsilber / Giuseppe Zaccai / Imre Berger / Ian Collinson / Christiane Schaffitzel /
Abstract: The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein ...The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein insertion. By employing an integrative approach combining small-angle neutron scattering (SANS), low-resolution electron microscopy and biophysical analyses we determined the arrangement of the proteins and lipids within the super-complex. The results guided the placement of X-ray structures of individual HTL components and allowed the proposal of a model of the functional translocon. Their arrangement around a central lipid-containing pool conveys an unexpected, but compelling mechanism for membrane-protein insertion. The periplasmic domains of YidC and SecD are poised at the protein-channel exit-site of SecY, presumably to aid the emergence of translocating polypeptides. The SecY lateral gate for membrane-insertion is adjacent to the membrane 'insertase' YidC. Absolute-scale SANS employing a novel contrast-match-point analysis revealed a dynamic complex adopting open and compact configurations around an adaptable central lipid-filled chamber, wherein polytopic membrane-proteins could fold, sheltered from aggregation and proteolysis.
History
DepositionNov 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.name / _em_software.version
Revision 1.2May 15, 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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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
Y: Protein translocase subunit SecY
E: Protein translocase subunit SecE
G: Protein-export membrane protein SecG
D: Protein translocase subunit SecD
F: Protein translocase subunit SecF
C: Membrane protein insertase YidC


Theoretical massNumber of molelcules
Total (without water)245,7456
Polymers245,7456
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area25910 Å2
ΔGint-179 kcal/mol
Surface area75270 Å2
MethodPISA

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Components

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Protein translocase subunit ... , 4 types, 4 molecules YEDF

#1: Protein Protein translocase subunit SecY


Mass: 50410.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: secY, prlA, b3300, JW3262 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AGA2
#2: Protein Protein translocase subunit SecE


Mass: 15248.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: secE, prlG, b3981, JW3944 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG96
#4: Protein Protein translocase subunit SecD


Mass: 67687.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: secD, b0408, JW0398 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG90
#5: Protein Protein translocase subunit SecF


Mass: 35413.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: secF, b0409, JW0399 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG93

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Protein , 2 types, 2 molecules GC

#3: Protein Protein-export membrane protein SecG / P12 / Preprotein translocase band 1 subunit


Mass: 14326.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: secG, b3175, JW3142 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG99
#6: Protein Membrane protein insertase YidC / Foldase YidC / Inner membrane protein YidC / Membrane integrase YidC / Oxa1Ec


Mass: 62658.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yidC, b3705, JW3683 / Production host: Escherichia coli (E. coli) / References: UniProt: P25714

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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

ComponentName: bacterial holo-translocon (HTL) / Type: COMPLEX
Details: Membrane Protein Complex consisting of SecYEG-SecDFYajC-YidC
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: PACEMBL_HTL3
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 5 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 10 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1EMAN2particle selection
2EPUimage acquisition
4BsoftCTF correction
10SPIDERinitial Euler assignment
11SPIDERfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 84732
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53648 / Symmetry type: POINT

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