+Open data
-Basic information
Entry | Database: PDB / ID: 7adm | ||||||
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Title | Structure of the mycoplasma MIB protein | ||||||
Components | Putative immunoglobulin-blocking virulence protein | ||||||
Keywords | MEMBRANE PROTEIN / Antibody binding protein / protease / protein complex. | ||||||
Function / homology | Mycoplasma virulence, signal domain / Putative immunoglobulin-blocking virulence protein / Mycoplasma virulence signal region (Myco_arth_vir_N) / IgG-blocking virulence domain / Putative immunoglobulin-blocking virulence protein Function and homology information | ||||||
Biological species | Mycoplasma mycoides subsp. capri (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Nottelet, P. / Bataille, L. / Gourgues, G. / Anger, R. / Lartigue, C. / Sirand-Pugnet, P. / Marza, E. / Fronzes, R. / Arfi, Y. | ||||||
Funding support | France, 1items
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Citation | Journal: Sci Adv / Year: 2021 Title: The mycoplasma surface proteins MIB and MIP promote the dissociation of the antibody-antigen interaction. Authors: Pierre Nottelet / Laure Bataille / Geraldine Gourgues / Robin Anger / Carole Lartigue / Pascal Sirand-Pugnet / Esther Marza / Remi Fronzes / Yonathan Arfi / Abstract: Mycoplasma immunoglobulin binding (MIB) and mycoplasma immunoglobulin protease (MIP) are surface proteins found in the majority of mycoplasma species, acting sequentially to capture antibodies and ...Mycoplasma immunoglobulin binding (MIB) and mycoplasma immunoglobulin protease (MIP) are surface proteins found in the majority of mycoplasma species, acting sequentially to capture antibodies and cleave off their V domains. Cryo-electron microscopy structures show how MIB and MIP bind to a Fab fragment in a "hug of death" mechanism. As a result, the orientation of the V and V domains is twisted out of alignment, disrupting the antigen binding site. We also show that MIB-MIP has the ability to promote the dissociation of the antibody-antigen complex. This system is functional in cells and protects mycoplasmas from antibody-mediated agglutination. These results highlight the key role of the MIB-MIP system in immunity evasion by mycoplasmas through an unprecedented mechanism, and open exciting perspectives to use these proteins as potential tools in the antibody field. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7adm.cif.gz | 214.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7adm.ent.gz | 172 KB | Display | PDB format |
PDBx/mmJSON format | 7adm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7adm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7adm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7adm_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 7adm_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/7adm ftp://data.pdbj.org/pub/pdb/validation_reports/ad/7adm | HTTPS FTP |
-Related structure data
Related structure data | 11731MC 7adjC 7adkC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 84962.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma mycoides subsp. capri (bacteria) Gene: MMC68F_00609 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A446C0S7 |
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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 |
-Sample preparation
Component | Name: Mycoplasma MIB protein in complex with a goat Fab / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mycoplasma mycoides subsp. capri str. GM12 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: Rosetta |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 0.77 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 65 |
-Processing
Software | Name: PHENIX / Version: 1.16_3546: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3517059 / Symmetry type: POINT | ||||||||||||||||||||||||
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