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- PDB-9slc: Closed conformation dome complex including the Sec-translocon (Se... -

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Basic information

Entry
Database: PDB / ID: 9slc
TitleClosed conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
Components
  • (Protein translocase subunit ...) x 2
  • (Uncharacterized lipoprotein ...) x 4
  • Probable protein-export membrane protein SecG
  • SecDF
  • SecE
KeywordsTRANSLOCASE / in-cell cryo-ET / Protein Folding / cell surface / Translocation / Sec-machinery
Function / homology
Function and homology information


cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / intracellular protein transmembrane transport / protein transport by the Sec complex / protein-transporting ATPase activity / protein import / protein secretion / transmembrane protein transporter activity / protein targeting ...cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / intracellular protein transmembrane transport / protein transport by the Sec complex / protein-transporting ATPase activity / protein import / protein secretion / transmembrane protein transporter activity / protein targeting / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / Family of unknown function (DUF6856) / Protein of unknown function DUF3713 / Protein of unknown function (DUF3713) / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain ...: / Family of unknown function (DUF6856) / Protein of unknown function DUF3713 / Protein of unknown function (DUF3713) / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA, C-terminal helicase domain / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA P-loop domain / SecA family signature. / SecA family profile. / SecA DEAD-like domain / SecA preprotein cross-linking domain / Protein translocase subunit SecY / Protein secY signature 1. / Protein secY signature 2. / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Prokaryotic membrane lipoprotein lipid attachment site profile. / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncharacterized protein MG055 homolog / Uncharacterized lipoprotein MG348 homolog / Uncharacterized lipoprotein MG338 homolog / Uncharacterized lipoprotein MG309 homolog / Uncharacterized lipoprotein MG307 homolog / Uncharacterized protein MG277 homolog / Protein translocase subunit SecA / Protein translocase subunit SecY / Probable protein-export membrane protein SecG
Similarity search - Component
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.1 Å
AuthorsJensen, R.K. / Xue, L. / Mahamid, J.
Funding support Denmark, United States, 2items
OrganizationGrant numberCountry
Danish Council for Independent Research0106-00010A Denmark
Chan Zuckerberg Initiative2021-234620 United States
CitationJournal: To Be Published
Title: In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex
Authors: Jensen, R.K. / Xue, L. / Marotta, F. / Somody, J.C. / Selkrig, J. / Lenz, S. / Rappsilber, J. / Savitski, M.M. / Kosinski, J. / Typas, A. / Zimmermann-Kogadeeva, M. / Bork, P. / Mahamid, J.
History
DepositionSep 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein translocase subunit SecA
B: Uncharacterized lipoprotein MG307 homolog
C: Uncharacterized lipoprotein MG309 homolog
D: SecDF
E: SecE
F: Uncharacterized lipoprotein MG338 homolog
G: Probable protein-export membrane protein SecG
I: Uncharacterized lipoprotein MG348 homolog
Y: Protein translocase subunit SecY
H: Uncharacterized lipoprotein MG348 homolog


Theoretical massNumber of molelcules
Total (without water)752,94510
Polymers752,94510
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, The assembly is supported by whole-cell crosslinking mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein translocase subunit ... , 2 types, 2 molecules AY

#1: Protein Protein translocase subunit SecA


Mass: 91942.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75559, protein-secreting ATPase
#9: Protein Protein translocase subunit SecY


Mass: 48965.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q59548

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Uncharacterized lipoprotein ... , 4 types, 5 molecules BCFIH

#2: Protein Uncharacterized lipoprotein MG307 homolog


Mass: 136216.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75342
#3: Protein Uncharacterized lipoprotein MG309 homolog


Mass: 143385.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75334
#6: Protein Uncharacterized lipoprotein MG338 homolog


Mass: 140427.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75296
#8: Protein Uncharacterized lipoprotein MG348 homolog


Mass: 30410.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75255

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Protein , 3 types, 3 molecules DEG

#4: Protein SecDF


Mass: 108345.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75387
#5: Protein SecE


Mass: 14489.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75048
#7: Protein Probable protein-export membrane protein SecG


Mass: 8352.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q9EXD0

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Closed conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
Type: CELL / Entity ID: #1-#2, #4-#9 / Source: NATURAL
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria) / Strain: 29342
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE
Details: Back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental chamber.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.9 e/Å2 / Avg electron dose per subtomogram: 125 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1Warp2.0.0volume selection
2SerialEMimage acquisition
4Warp2.0.0CTF correction
7PowerFitmodel fitting
8UCSF ChimeraXmodel fitting
12Warp2.0.0final Euler assignment
13RELION4.0.1classificationRELION 3D classificaiton
14Warp2.0.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11557 / Num. of class averages: 2 / Symmetry type: POINT
EM volume selectionMethod: Manual picking and Deep-learning based particle picking
Details: Initial particles were manually picked and used to generate training data for iterative rounds of DeePiCt particle picking and junk cleaning with 3D classification in RELION. A final round ...Details: Initial particles were manually picked and used to generate training data for iterative rounds of DeePiCt particle picking and junk cleaning with 3D classification in RELION. A final round of multi-class particle picking was performed in DeepFinder followed by manual curation of the final particle positions. Subtomograms were extracted in Warp.
Num. of tomograms: 355 / Num. of volumes extracted: 13770 / Reference model: Data-driven, Iteratively improved
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Fitting was performed using PowerFit and Fit-in-map in ChimeraX
Atomic model buildingSource name: AlphaFold / Type: in silico model

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