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- EMDB-5835: A Unique Human Mycoplasma Protein that Generically Blocks Antigen... -

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Basic information

Entry
Database: EMDB / ID: EMD-5835
TitleA Unique Human Mycoplasma Protein that Generically Blocks Antigen-Antibody Union
Map dataReconstruction of MG281T in complex with Fab 13PL
Sample
  • Sample: MG281T in complex with Fab 13PL
  • Protein or peptide: MG281T
  • Protein or peptide: Fab 13PL
Function / homology
Function and homology information


IgG-blocking protein M / : / : / : / Protein M, large region / Protein M, smaller domain / Protein M, C-terminal / IgG-blocking virulence domain
Similarity search - Domain/homology
Uncharacterized protein MG281
Similarity search - Component
Biological speciesMycoplasma genitalium (bacteria) / unidentified (others)
Methodsingle particle reconstruction / negative staining / Resolution: 19.0 Å
AuthorsGrover RK / Zhu X / Nieusma T / Jones T / Boreo I / MacLeod AS / Mark A / Niessen S / Kim HJ / Kong L ...Grover RK / Zhu X / Nieusma T / Jones T / Boreo I / MacLeod AS / Mark A / Niessen S / Kim HJ / Kong L / Assad-Garcia N / Kwon K / Chesi M / Salomon DR / Jelinek DF / Kyle RA / Pyles RB / Glass JI / Ward AB / Wilson IA / Lerner RA
CitationJournal: Science / Year: 2014
Title: A structurally distinct human mycoplasma protein that generically blocks antigen-antibody union.
Authors: Rajesh K Grover / Xueyong Zhu / Travis Nieusma / Teresa Jones / Isabel Boreo / Amanda S MacLeod / Adam Mark / Sherry Niessen / Helen J Kim / Leopold Kong / Nacyra Assad-Garcia / Keehwan Kwon ...Authors: Rajesh K Grover / Xueyong Zhu / Travis Nieusma / Teresa Jones / Isabel Boreo / Amanda S MacLeod / Adam Mark / Sherry Niessen / Helen J Kim / Leopold Kong / Nacyra Assad-Garcia / Keehwan Kwon / Marta Chesi / Vaughn V Smider / Daniel R Salomon / Diane F Jelinek / Robert A Kyle / Richard B Pyles / John I Glass / Andrew B Ward / Ian A Wilson / Richard A Lerner /
Abstract: We report the discovery of a broadly reactive antibody-binding protein (Protein M) from human mycoplasma. The crystal structure of the ectodomain of transmembrane Protein M differs from other known ...We report the discovery of a broadly reactive antibody-binding protein (Protein M) from human mycoplasma. The crystal structure of the ectodomain of transmembrane Protein M differs from other known protein structures, as does its mechanism of antibody binding. Protein M binds with high affinity to all types of human and nonhuman immunoglobulin G, predominantly through attachment to the conserved portions of the variable region of the κ and λ light chains. Protein M blocks antibody-antigen union, likely because of its large C-terminal domain extending over the antibody-combining site, blocking entry to large antigens. Similar to the other immunoglobulin-binding proteins such as Protein A, Protein M as well as its orthologs in other Mycoplasma species could become invaluable reagents in the antibody field.
History
DepositionDec 13, 2013-
Header (metadata) releaseMar 19, 2014-
Map releaseMar 19, 2014-
UpdateMar 19, 2014-
Current statusMar 19, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.73
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.73
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5835.gif

Downloads & links

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Map

FileDownload / File: emd_5835.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of MG281T in complex with Fab 13PL
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 120 pix.
= 246. Å		2.05 Å/pix.
x 120 pix.
= 246. Å		2.05 Å/pix.
x 120 pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.73 / Movie #1: 3.73
Minimum - Maximum-3.59377337 - 10.903564449999999
Average (Standard dev.)0.0 (±0.69299376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-29-29-29
Dimensions120120120
Spacing120120120
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z246.000246.000246.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-29-29-29
NC/NR/NS120120120
D min/max/mean-3.59410.904-0.000

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Supplemental data

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Sample components

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Entire : MG281T in complex with Fab 13PL

EntireName: MG281T in complex with Fab 13PL
Components
  • Sample: MG281T in complex with Fab 13PL
  • Protein or peptide: MG281T
  • Protein or peptide: Fab 13PL

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Supramolecule #1000: MG281T in complex with Fab 13PL

SupramoleculeName: MG281T in complex with Fab 13PL / type: sample / ID: 1000
Oligomeric state: one monomer of MG281T binds to one monomer of Fab 13PL
Number unique components: 2
Molecular weightExperimental: 100 KDa / Theoretical: 100 KDa / Method: Western blot

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Macromolecule #1: MG281T

MacromoleculeName: MG281T / type: protein_or_peptide / ID: 1 / Name.synonym: protein M / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Mycoplasma genitalium (bacteria) / synonym: human mycoplasma
Molecular weightExperimental: 50 KDa / Theoretical: 50 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Uncharacterized protein MG281

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Macromolecule #2: Fab 13PL

MacromoleculeName: Fab 13PL / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
StainingType: NEGATIVE
Details: 3 uL 2% uranyl formate was added to grids adsorbed with 3uL protein sample, then blotted and air-dried.
GridDetails: 400-Cu copper mesh with thin nitrocellulose support and thin carbon, glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
TemperatureAverage: 298 K
Alignment procedureLegacy - Astigmatism: Objective astigmatism was corrected at 100,000 time magnification using a live feed of the power spectrum.
Specialist opticsEnergy filter - Name: FEI
DateSep 20, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 56
Details: 36 images were collected at each angle in 5 degree intervals from 0 degrees to -55 degrees.
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -0.7 µm / Nominal defocus min: -0.7 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle min: -55

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Image processing

DetailsParticles were selected using automatic (difference-of-Gaussians) picking followed by reference-free classification to eliminate noisy picks or non-target aggregation states.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: OTHER / Software - Name: Appion, spider, EMAN1, Xmipp, EMAN2 / Number images used: 10138
Final two d classificationNumber classes: 68

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Atomic model buiding 1

Initial modelPDB ID:

4nzr


Chain - #0 - Chain ID: H / Chain - #1 - Chain ID: L / Chain - #2 - Chain ID: M
SoftwareName: Chimera
DetailsThe crystal structure was docked to the EM volume using the fitting function in UCSF Chimera.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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