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- PDB-7adm: Structure of the mycoplasma MIB protein -

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Basic information

Entry
Database: PDB / ID: 7adm
TitleStructure of the mycoplasma MIB protein
ComponentsPutative immunoglobulin-blocking virulence protein
KeywordsMEMBRANE PROTEIN / Antibody binding protein / protease / protein complex.
Function / homologyMycoplasma 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 speciesMycoplasma mycoides subsp. capri (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsNottelet, P. / Bataille, L. / Gourgues, G. / Anger, R. / Lartigue, C. / Sirand-Pugnet, P. / Marza, E. / Fronzes, R. / Arfi, Y.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: 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
DepositionSep 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release

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Structure visualization

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  • EMDB-11731
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Assembly

Deposited unit
C: Putative immunoglobulin-blocking virulence protein


Theoretical massNumber of molelcules
Total (without water)84,9631
Polymers84,9631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area31120 Å2

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Components

#1: Protein Putative immunoglobulin-blocking virulence 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

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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: Mycoplasma MIB protein in complex with a goat Fab / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycoplasma mycoides subsp. capri str. GM12 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: Rosetta
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 0.77 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 65

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Processing

SoftwareName: PHENIX / Version: 1.16_3546: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
9PHENIXmodel refinement
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3517059 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045021
ELECTRON MICROSCOPYf_angle_d0.6936770
ELECTRON MICROSCOPYf_dihedral_angle_d11.8083058
ELECTRON MICROSCOPYf_chiral_restr0.047717
ELECTRON MICROSCOPYf_plane_restr0.004897

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