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- PDB-9qgq: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pne... -

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Basic information

Entry
Database: PDB / ID: 9qgq
TitleHomotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae
ComponentsHomotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae
KeywordsMEMBRANE PROTEIN / Lipoprotein Mycoplasma pneumoniae PPIase Homotrimer
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsManger, S. / Keles, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Structure of the essential Mycoplasma pneumoniae lipoprotein Mpn444 reveals a peptidyl-prolyl isomerase domain involved in extracellular protein folding
Authors: Manger, S. / Keles, I. / Frangakis, A.S.
History
DepositionMar 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae
B: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae
C: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae


Theoretical massNumber of molelcules
Total (without water)353,8303
Polymers353,8303
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae


Mass: 117943.305 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasmoides pneumoniae M129 (bacteria)
Gene: mpn444 / Production host: Escherichia coli (E. coli)
Has protein modificationN

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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: Homotrimer of the extracellular PPIase Mpn444 from Mycoplasma pneumoniae
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Details: 20 mM Tris pH 7.4, 200 mM NaCl and 0-0.01 % LMNG or 1 mM CHAPSO
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Whatman 595 filter papers were incubated for 1 h in the Vitrobot chamber at 100% relative humidity and 277 K prior to plunge freezing.

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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: 105000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.5.3particle selection
2SerialEMv4.1.0 betaimage acquisition
4cryoSPARCv4.5.3CTF correction
10cryoSPARCv4.5.3initial Euler assignment
11cryoSPARCv4.5.3final Euler assignment
12cryoSPARCv4.5.3classification
13cryoSPARCv4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3376184
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 506291 / Symmetry type: POINT

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