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- EMDB-11729: CryoEM structure of MIB-MIP in complex with a polyclonal goat Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-11729
TitleCryoEM structure of MIB-MIP in complex with a polyclonal goat Fab
Map data
Sample
  • Complex: Mycoplasma MIB-MIP proteins in complex with a goat Fab
    • Protein or peptide: Putative immunoglobulin-blocking virulence protein
    • Protein or peptide: Lipoprotein
KeywordsAntibody binding protein / protease / protein complex. / MEMBRANE PROTEIN
Function / homologyUncharacterised protein family MG067 / Mycoplasma peptidase DUF31 / Mycoplasma peptidase (DUF31) / 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 / Lipoprotein
Function and homology information
Biological speciesMycoplasma mycoides subsp. capri str. GM12 (bacteria) / Mycoplasma mycoides subsp. capri (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsNottelet P / Bataille L
Funding support France, 1 items
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, 2020-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7adk
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7adk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11729.png

Downloads & links

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Map

FileDownload / File: emd_11729.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-24.763587999999999 - 29.809916000000001
Average (Standard dev.)0.000000000003581 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z212.480212.480212.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-24.76429.8100.000

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Supplemental data

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Additional map: #1

Fileemd_11729_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: #1

Fileemd_11729_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11729_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycoplasma MIB-MIP proteins in complex with a goat Fab

EntireName: Mycoplasma MIB-MIP proteins in complex with a goat Fab
Components
  • Complex: Mycoplasma MIB-MIP proteins in complex with a goat Fab
    • Protein or peptide: Putative immunoglobulin-blocking virulence protein
    • Protein or peptide: Lipoprotein

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Supramolecule #1: Mycoplasma MIB-MIP proteins in complex with a goat Fab

SupramoleculeName: Mycoplasma MIB-MIP proteins in complex with a goat Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycoplasma mycoides subsp. capri str. GM12 (bacteria)

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Macromolecule #1: Putative immunoglobulin-blocking virulence protein

MacromoleculeName: Putative immunoglobulin-blocking virulence protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma mycoides subsp. capri (bacteria)
Molecular weightTheoretical: 84.962719 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: VYFLKKKKNK ILTIALVASL AASVSFGSVL YYSFSDNHIS FDTSSNGITD AELAPINNAI NDAIVSNRDN KLKPSEEKII KETEKKIEE KIIIPPAKKE EKIEAAKPIP KPVVRKPETK ITSPKITRRK QTITIAGIEV EAEIEGPPGF VTHQRDKDRK I SNPTKPYQ ...String:
VYFLKKKKNK ILTIALVASL AASVSFGSVL YYSFSDNHIS FDTSSNGITD AELAPINNAI NDAIVSNRDN KLKPSEEKII KETEKKIEE KIIIPPAKKE EKIEAAKPIP KPVVRKPETK ITSPKITRRK QTITIAGIEV EAEIEGPPGF VTHQRDKDRK I SNPTKPYQ NHTVNKILSV KVTDKLKEQV AKDALSGGNG YDEGVGLFNN SIFNVFKEEF NSGKELNDIL SSLESVARQN SG AFQNTLE RYKKMLDSNN VINFLKSEAQ KEYPKLKSKF QTKNQEYIWL IANLDQSKFT KIASTSEKYL EKGLTISPRS AFI NEAGEI DSNGWGPPDE YNTVTSRLRR DNSEYRVFDY DEYYSRSSDR IANGTYPGWV KEDVSEPYSK KYNFKASDGI RFSK LERIN PNPAKGKLNS GLVLDLDVSN DEAYRRSKEL IEKLQKDGEQ ITSYRIKNMG EKNSDQAFKD ILGALPKDIQ QLELF FSDK ATNTASLIAL ENKNIKELSL YTSGNSLKKA WSYNPLALRN TTWINTIDYN VSAEYSSHDK ITTRITFNTL AFDQED FSN GSYERINDGL RMVYYARNNE PFFQGGHGPG LEPDKKLGQN SYPTGLDFSR VTGIKSLKGL RFDDDLDTSN EPRKITE LT LYNNESYFEI SSDELNEANL QHLSTGEGNP EKPKIHFSNG NNTTSIRISG KTLLSDEGRR NLDKYFEYNE SLRNSGKQ I QIPNGSDELK KQLEGWGYKV STASDRSFT

UniProtKB: Putative immunoglobulin-blocking virulence protein

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Macromolecule #2: Lipoprotein

MacromoleculeName: Lipoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasma mycoides subsp. capri (bacteria)
Molecular weightTheoretical: 98.559016 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKRLNKLLMY ISSSTLLLPI TLLVACTPSK VVAKPINDDE FNKLIDSIKT ENDLLKYADI RFKNPNGADT KKEDIIPSQL KSENISITF KGKYQGQISA VVTNVDVDRT NPFAVQNEAT IFVQFKNLKT NTSKPISITI KGLNQKGNFD ASGNIVVDDF A YFGGTSGY ...String:
MKRLNKLLMY ISSSTLLLPI TLLVACTPSK VVAKPINDDE FNKLIDSIKT ENDLLKYADI RFKNPNGADT KKEDIIPSQL KSENISITF KGKYQGQISA VVTNVDVDRT NPFAVQNEAT IFVQFKNLKT NTSKPISITI KGLNQKGNFD ASGNIVVDDF A YFGGTSGY DEYTKKDQKS RFDYDNERYM TRLKSQFGNS SNSINLKEYR GLETKQENIK KFDDQAAISN FDTYYNAALK GF TLPVYGS DGKVSGLKIY EGAEIGKGPS VVDSLGRNEK AKTVGLARTL PNEEYKTSAI QTFQTNFTIY KDYEKEIEEA EDN IKLFDS WNEQQIQSYI SAQLTQLRLN YEDEVSQIDR EISQTQPDKT TILSNLNQKK SKIESEYQKE LSTISKLNKD SLKE WQRKE IEKYNEKKKE KTFQISESGT MWIMDYLDEN AGKNPTKFYF GTNSHVAKGI KDGMVSFSLT RLNSEVKVGQ TFKLN GHDS NFTKFTFSPI NGNKLEDAVT AIFHATDFIN ENSSPLKLLD SEQKSKYNGA GIFADFAIVE VDFAKLLDKG KYSYSV WSA SNDITNQYET EQNKLISKIT NNYSESDKKV KFFSDSLLNE QTYAKFDRPL DFDPKKEDEL KKYNDLDSLY IVGYPTA YK DFYLDQYEDE KQLKNKKYDF SLWINSEYKF YNKLINKEGS TNSFKEYETG KGNFFSYQIG YRSFIDKPGL TDAFITVN K VGKKLYSLKD KNKNEVKKYF NYGLEILPRF YAPAGGASGS SVRTKDNKLL AVYHASNETA RTGLAVAFRS DGYDYKNLF GDYKLGQYDL IYGGGKDQQK EKSYREVMNK MYSGKKSALF QNGFTDDKIP SEFKFNNGTQ N

UniProtKB: Lipoprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.45 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 255911
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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