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

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Entry
Database: PDB / ID: 5mg3
TitleEM fitted model of bacterial holo-translocon
DescriptorProtein translocase subunit SecY
Protein translocase subunit SecE
Protein-export membrane protein SecG
Protein translocase subunit SecD
Protein translocase subunit SecF
Membrane protein insertase YidC
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 A resolution / Single particle)
AuthorsSchaffitzel, C. / Botte, M.
CitationSci Rep, 2016, 6, 38399-38399

Sci Rep, 2016, 6, 38399-38399 StrPapers
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

DateDeposition: Nov 20, 2016 / Release: Dec 28, 2016

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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 (A2)25910
ΔGint (kcal/M)-179
Surface area (A2)75270
MethodPISA

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Components

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Polypeptide(L) , 6 types, 6 molecules YEGDFC

#1: Polypeptide(L)Protein translocase subunit SecY


Mass: 50410.523 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0AGA2
#2: Polypeptide(L)Protein translocase subunit SecE


Mass: 15248.021 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0AG96
#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
#4: Polypeptide(L)Protein translocase subunit SecD


Mass: 67687.984 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0AG90
#5: Polypeptide(L)Protein translocase subunit SecF


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: bacterial holo-translocon (HTL)
Details: Membrane Protein Complex consisting of SecYEG-SecDFYajC-YidC
Type: COMPLEX
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100

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Electron microscopy imaging

MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD

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Processing

3D reconstructionResolution: 14 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 53648

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