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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
DescriptorProtein-export membrane protein SecG
Membrane protein insertase YidC
(Protein translocase subunit ...) x 4
KeywordsCHAPERONE / holotranslocon / membrane protein insertion machinery / chaperone / protein secretion
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (14 Å resolution / Particle / Single particle)
AuthorsSchaffitzel, C. / Botte, M.
CitationSci Rep, 2016, 6, 38399-38399

Sci Rep, 2016, 6, 38399-38399 Yorodumi Papers
A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion.
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 20, 2016 / Release: Dec 28, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 28, 2016Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collectionem_image_scans / em_software_em_software.name / _em_software.version

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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
Polyers245,7456
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)25910
ΔGint (kcal/M)-179
Surface area (Å2)75270
MethodPISA

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Components

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

#1: Polypeptide(L)Protein translocase subunit SecY


Mass: 50410.523 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0AGA2

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)
#2: Polypeptide(L)Protein translocase subunit SecE


Mass: 15248.021 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0AG96

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)
#4: Polypeptide(L)Protein translocase subunit SecD


Mass: 67687.984 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0AG90

Cellular component

Molecular function

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

Biological process

#5: Polypeptide(L)Protein translocase subunit SecF


Mass: 35413.250 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0AG93

Cellular component

Molecular function

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

Biological process

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Polypeptide(L) , 2 types, 2 molecules GC

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


Mass: 14326.448 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0AG99

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)
#6: Polypeptide(L)Membrane protein insertase YidC / Foldase YidC / Inner membrane protein YidC / Membrane integrase YidC / Oxa1Ec


Mass: 62658.582 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P25714

Cellular component

Molecular function

Biological process

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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: bacterial holo-translocon (HTL) / Type: COMPLEX
Details: Membrane Protein Complex consisting of SecYEG-SecDFYajC-YidC
Entity ID: 1, 2, 3, 4, 5, 6 / Source: RECOMBINANT
Molecular weightValue: 0.25 deg. / Units: MEGADALTONS / Experimental value: YES
Source (natural)Organism: Escherichia coli
Source (recombinant)Organism: Escherichia 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 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: 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
IDNameVersionCategoryImage processing IDImaging ID
1EMAN2PARTICLE SELECTION1
2EPUIMAGE ACQUISITION1
4BsoftCTF CORRECTION1
10SPIDERINITIAL EULER ASSIGNMENT1
11SPIDERFINAL EULER ASSIGNMENT1
13RELIONRECONSTRUCTION1
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNumber of particles selected: 84732
SymmetryPoint symmetry: C1
3D reconstructionResolution: 14 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 53648 / Symmetry type: POINT

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