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- PDB-9gnh: Cryo-EM structure of essential Mycoplasma pneumoniae lipoprotein ... -

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Basic information

Entry
Database: PDB / ID: 9gnh
TitleCryo-EM structure of essential Mycoplasma pneumoniae lipoprotein Mpn444 homotrimer
ComponentsUncharacterized lipoprotein MG309 homolog
KeywordsUNKNOWN FUNCTION / Lipoprotein Surface Protein Mycoplasma pneumoniae
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: 5.4 Å
AuthorsManger, S. / Keles, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 2566/1 Germany
CitationJournal: To Be Published
Title: Structural characterization of an essential lipoprotein of Mycoplasma pneumoniae
Authors: Keles, I. / Manger, S. / Frangakis, A.S.
History
DepositionSep 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized lipoprotein MG309 homolog
B: Uncharacterized lipoprotein MG309 homolog
C: Uncharacterized lipoprotein MG309 homolog


Theoretical massNumber of molelcules
Total (without water)434,4023
Polymers434,4023
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: 144800.641 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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 homotrimer
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-HCl 200 mM NaCl 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: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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 BIOCONTINUUM (6k x 4k) / Num. of real images: 7811

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2SerialEM4.1.0betaimage acquisition
4cryoSPARC4.5.3CTF correction
10cryoSPARC4.5.3initial Euler assignment
11cryoSPARC4.5.3final Euler assignment
12cryoSPARC4.5.3classification
13cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3376184
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 626110 / Symmetry type: POINT

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