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- PDB-9srq: Full-length cryo-EM structure of essential Mycoplasma pneumoniae ... -

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Basic information

Entry
Database: PDB / ID: 9srq
TitleFull-length cryo-EM structure of essential Mycoplasma pneumoniae lipoprotein Mpn444
ComponentsUncharacterized lipoprotein MG309 homolog
KeywordsCHAPERONE / PPIase Chaperone Mycoplasma pneumoniae lipoprotein
Function / homologyProtein of unknown function DUF3713 / Protein of unknown function (DUF3713) / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / Uncharacterized lipoprotein MG309 homolog
Function and homology information
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsManger, S. / Keles, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 2566/1 Germany
CitationJournal: To Be Published
Title: Structures of the essential Mycoplasma pneumoniae lipoproteins Mpn444 and Mpn436 reveal a peptidyl-prolyl isomerase domain involved in extracellular protein folding
Authors: Manger, S. / Keles, I. / Frangakis, A.S. / Scheffer, M.P. / Mantanya, M.S.
History
DepositionSep 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Uncharacterized lipoprotein MG309 homolog


Theoretical massNumber of molelcules
Total (without water)146,4421
Polymers146,4421
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 Uncharacterized lipoprotein MG309 homolog


Mass: 146441.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Full-length protein without N-terminal signal peptide
Source: (gene. exp.) Mycoplasmoides pneumoniae M129 (bacteria)
Gene: MPN_444, H08_orf1325, MP397 / Production host: Escherichia coli (E. coli) / References: UniProt: P75334
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: Essential Mycoplasma pneumoniae lipoprotein Mpn444 / Type: COMPLEX
Details: Recombinantly expressed in E.coli without the N-terminal signal peptide
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.145 MDa / Experimental 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 to 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 type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K
Details: Nominal blot force -3 Wait time 10 s Blotting time 14 s Before freezing, Whatman 595 filter papers were incubated for 1 h in the Vitrobot chamber at 100% relative humidity and 278K.

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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: 3600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 2.5 sec. / Electron 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
7ISOLDEmodel fitting
9cryoSPARCv4.5.3initial Euler assignment
10cryoSPARCv4.5.3final Euler assignment
11cryoSPARCv4.5.3classification
12cryoSPARCv4.5.33D reconstruction
13PHENIXmodel refinement
14Cootmodel refinement
Image processingDetails: The camera was operated in dose-fractionation counting mode with a dose rate of ~16 electrons per A2 per s, resulting in a total dose of 50 electrons per A2. The frame time was adjusted to 1 ...Details: The camera was operated in dose-fractionation counting mode with a dose rate of ~16 electrons per A2 per s, resulting in a total dose of 50 electrons per A2. The frame time was adjusted to 1 frame per 1 electron per A2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6832694
3D reconstructionResolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 432841 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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