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- PDB-8pbx: Single particle cryo-EM of the P140-P110 heterodimer of Mycoplasm... -

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Basic information

Entry
Database: PDB / ID: 8pbx
TitleSingle particle cryo-EM of the P140-P110 heterodimer of Mycoplasma genitalium at 3.3 Angstrom resolution.
Components
  • Adhesin P1
  • Mgp-operon protein 3
KeywordsCELL ADHESION / Adhesion / Mycoplasma genitalium
Function / homology
Function and homology information


adhesion of symbiont to microvasculature / cell adhesion / plasma membrane
Similarity search - Function
Adhesin P1, C-terminal domain / Adhesin P1, N-terminal / Adhesin P1 / Mycoplasma adhesin P1, C-terminal / Mycoplasma adhesin P1, N-terminal / MgpC adhesin / Mgp-operon protein 3, C-terminal domain / MgpC adhesin / MGP3 C-terminal domain
Similarity search - Domain/homology
Adhesin P1 / Mgp-operon protein 3
Similarity search - Component
Biological speciesMycoplasmoides genitalium G37 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSprankel, L. / Scheffer, M.P. / Frangakis, A.S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)FR 1653/6-3 Germany
German Research Foundation (DFG)GRK 2566/1 Germany
CitationJournal: PLoS Pathog / Year: 2023
Title: Cryo-electron tomography reveals the binding and release states of the major adhesion complex from Mycoplasma genitalium.
Authors: Lasse Sprankel / Margot P Scheffer / Sina Manger / Utz H Ermel / Achilleas S Frangakis /
Abstract: The nap particle is an immunogenic surface adhesion complex from Mycoplasma genitalium. It is essential for motility and responsible for binding sialylated oligosaccharides on the surface of the host ...The nap particle is an immunogenic surface adhesion complex from Mycoplasma genitalium. It is essential for motility and responsible for binding sialylated oligosaccharides on the surface of the host cell. The nap particle is composed of two P140-P110 heterodimers, the structure of which was recently solved. However, the interpretation of the mechanism by which the mycoplasma cells orchestrate adhesion remained challenging. Here, we provide cryo-electron tomography structures at ~11 Å resolution, which allow for the distinction between the bound and released state of the nap particle, displaying the in vivo conformational states. Fitting of the atomically resolved structures reveals that bound sialylated oligosaccharides are stabilized by both P110 and P140. Movement of the stalk domains allows for the transfer of conformational changes from the interior of the cell to the binding pocket, thus having the capability of an active release process. It is likely that the same mechanism can be transferred to other Mycoplasma species that belong to the pneumoniae cluster.
History
DepositionJun 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mgp-operon protein 3
B: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)275,1912
Polymers275,1912
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Mgp-operon protein 3 / Mgp3 / ORF-3 protein


Mass: 115382.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasmoides genitalium G37 (bacteria)
Gene: MG192 / Production host: Mycoplasmoides genitalium G37 (bacteria) / References: UniProt: P22747
#2: Protein Adhesin P1 / Attachment protein / Cytadhesin P1 / MgPa


Mass: 159809.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides genitalium G37 (bacteria) / References: UniProt: P20796

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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

Component
IDNameTypeEntity IDParent-IDSource
1P140-P110 HeterodimerCOMPLEXall0MULTIPLE SOURCES
2Mgp-operon protein 3COMPLEX#11RECOMBINANT
3Adhesin P1COMPLEX#21NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Mycoplasmoides genitalium G37 (bacteria)243273
33Mycoplasmoides genitalium G37 (bacteria)243273
Source (recombinant)Organism: Mycoplasmoides genitalium G37 (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
175 mMTris1
2400 mMsodium chlorideNaClSodium chloride1
35 %Glycerol1
40.5 %octylglucoside detergent1
SpecimenConc.: 0.025 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: 277.15 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 FIELDBright-field microscopy / Nominal magnification: 130000 X / Calibrated magnification: 130000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 4000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum SE / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.2particle selection
4cryoSPARC3.3.2CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARC3.3.2initial Euler assignment
11cryoSPARC3.3.2final Euler assignment
12cryoSPARC3.3.2classification
13cryoSPARC3.3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149542 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDChain-IDChain residue rangePdb chain residue range
16RUT

6rut

6RUT1
26R3T

6r3t

A6R3T2A818-936818-936
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 85.61 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004617391
ELECTRON MICROSCOPYf_angle_d0.543223670
ELECTRON MICROSCOPYf_chiral_restr0.04242627
ELECTRON MICROSCOPYf_plane_restr0.00393110
ELECTRON MICROSCOPYf_dihedral_angle_d4.80192301

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