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Open data
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Basic information
Entry | Database: PDB / ID: 7bwm | ||||||||||||||||||||||||
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Title | Cryo-EM structure of the human pathogen Mycoplasma pneumoniae P1 | ||||||||||||||||||||||||
![]() | Adhesin P1 | ||||||||||||||||||||||||
![]() | STRUCTURAL PROTEIN / Sialic acid receptor | ||||||||||||||||||||||||
Function / homology | ![]() attachment organelle / adhesion of symbiont to microvasculature / cell projection / cell surface / membrane / plasma membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||||||||
![]() | Kawamoto, A. / Kenri, T. / Namba, K. / Miyata, M. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.5 KB | Display | ![]() |
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PDB format | ![]() | 227.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 715.9 KB | Display | ![]() |
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Full document | ![]() | 732.5 KB | Display | |
Data in XML | ![]() | 36.6 KB | Display | |
Data in CIF | ![]() | 56.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30233MC ![]() 6rc9C ![]() 6rj1C ![]() 6tlzC ![]() 6tm0C M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 8.0 TB Data #1: Unaligned 136-frame movies of human pathogen Mycoplasma pneumoniae P1 [micrographs - multiframe] Data #2: Unaligned 78-frame movies of human pathogen Mycoplasma pneumoniae P1 [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 143778.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P11311 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Nap protein P1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 170 kDa/nm / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 78.9 K / Temperature (min): 78.9 K |
Image recording | Average 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 optics | Spherical aberration corrector: Microscope was modified with a Cs corrector |
Image scans | Width: 4096 / Height: 4096 |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68014 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6RC9 Accession code: 6RC9 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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