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- PDB-7bwm: Cryo-EM structure of the human pathogen Mycoplasma pneumoniae P1 -

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Basic information

Entry
Database: PDB / ID: 7bwm
TitleCryo-EM structure of the human pathogen Mycoplasma pneumoniae P1
ComponentsAdhesin P1
KeywordsSTRUCTURAL PROTEIN / Sialic acid receptor
Function / homology
Function and homology information


attachment organelle / adhesion of symbiont to microvasculature / cell projection / cell surface / membrane / 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
Similarity search - Domain/homology
Biological speciesMycoplasma pneumoniae M129 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKawamoto, A. / Kenri, T. / Namba, K. / Miyata, M.
Funding support Japan, 7items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25000013 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
Japan Society for the Promotion of Science (JSPS)24117002 Japan
Japan Society for the Promotion of Science (JSPS)24390107 Japan
Japan Society for the Promotion of Science (JSPS)17H01544 Japan
Japan Society for the Promotion of Science (JSPS)JPMJCR19S5 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Immunodominant proteins P1 and P40/P90 from human pathogen Mycoplasma pneumoniae.
Authors: David Vizarraga / Akihiro Kawamoto / U Matsumoto / Ramiro Illanes / Rosa Pérez-Luque / Jesús Martín / Rocco Mazzolini / Paula Bierge / Oscar Q Pich / Mateu Espasa / Isabel Sanfeliu / ...Authors: David Vizarraga / Akihiro Kawamoto / U Matsumoto / Ramiro Illanes / Rosa Pérez-Luque / Jesús Martín / Rocco Mazzolini / Paula Bierge / Oscar Q Pich / Mateu Espasa / Isabel Sanfeliu / Juliana Esperalba / Miguel Fernández-Huerta / Margot P Scheffer / Jaume Pinyol / Achilleas S Frangakis / Maria Lluch-Senar / Shigetarou Mori / Keigo Shibayama / Tsuyoshi Kenri / Takayuki Kato / Keiichi Namba / Ignacio Fita / Makoto Miyata / David Aparicio /
Abstract: Mycoplasma pneumoniae is a bacterial human pathogen that causes primary atypical pneumonia. M. pneumoniae motility and infectivity are mediated by the immunodominant proteins P1 and P40/P90, which ...Mycoplasma pneumoniae is a bacterial human pathogen that causes primary atypical pneumonia. M. pneumoniae motility and infectivity are mediated by the immunodominant proteins P1 and P40/P90, which form a transmembrane adhesion complex. Here we report the structure of P1, determined by X-ray crystallography and cryo-electron microscopy, and the X-ray structure of P40/P90. Contrary to what had been suggested, the binding site for sialic acid was found in P40/P90 and not in P1. Genetic and clinical variability concentrates on the N-terminal domain surfaces of P1 and P40/P90. Polyclonal antibodies generated against the mostly conserved C-terminal domain of P1 inhibited adhesion of M. pneumoniae, and serology assays with sera from infected patients were positive when tested against this C-terminal domain. P40/P90 also showed strong reactivity against human infected sera. The architectural elements determined for P1 and P40/P90 open new possibilities in vaccine development against M. pneumoniae infections.
History
DepositionApr 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: Adhesin P1


Theoretical massNumber of molelcules
Total (without water)143,7781
Polymers143,7781
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area43940 Å2

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Components

#1: Protein Adhesin P1 / Attachment protein / Cytadhesin P1


Mass: 143778.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae M129 (bacteria) / Strain: M129 / Gene: mgpA, MPN_141, MP013
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P11311

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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: Nap protein P1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 170 kDa/nm / Experimental value: NO
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: 96000 X / Nominal defocus max: 2750 nm / Nominal defocus min: 750 nm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 78.9 K / Temperature (min): 78.9 K
Image recordingAverage exposure time: 36.33 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 5279
EM imaging opticsSpherical aberration corrector: Microscope was modified with a Cs corrector
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameVersionCategory
1Gautomatchparticle selection
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68014 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6RC9

6rc9


Accession code: 6RC9 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0059774
ELECTRON MICROSCOPYf_angle_d0.6613331
ELECTRON MICROSCOPYf_dihedral_angle_d17.3163515
ELECTRON MICROSCOPYf_chiral_restr0.0451446
ELECTRON MICROSCOPYf_plane_restr0.0051761

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