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- EMDB-5834: A Unique Human Mycoplasma Protein that Generically Blocks Antigen... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5834 | |||||||||
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Title | A Unique Human Mycoplasma Protein that Generically Blocks Antigen-Antibody Union | |||||||||
![]() | Protein M and Fab b12 | |||||||||
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Function / homology | IgG-blocking protein M / : / Protein M, large region / IgG-blocking virulence domain / membrane / Uncharacterized protein MG281![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 21.3 Å | |||||||||
![]() | Grover 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 | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 626 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.6 KB 12.6 KB | Display Display | ![]() |
Images | ![]() ![]() | 21.9 KB 2.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 79.4 KB | Display | ![]() |
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Full document | ![]() | 78.5 KB | Display | |
Data in XML | ![]() | 493 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Protein M and Fab b12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Fab of human mAb b12 in complex with Full length MG281
Entire | Name: Fab of human mAb b12 in complex with Full length MG281 |
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Components |
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-Supramolecule #1000: Fab of human mAb b12 in complex with Full length MG281
Supramolecule | Name: Fab of human mAb b12 in complex with Full length MG281 type: sample / ID: 1000 Oligomeric state: one monomer of MG281 binds to one Fab monomer Number unique components: 2 |
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Molecular weight | Theoretical: 100 KDa / Method: Western blot |
-Macromolecule #1: MG281
Macromolecule | Name: MG281 / type: protein_or_peptide / ID: 1 / Name.synonym: protein M / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 50 KDa / Theoretical: 50 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Uncharacterized protein MG281 |
-Macromolecule #2: mAb b12 Fab
Macromolecule | Name: mAb b12 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Staining | Type: NEGATIVE Details: 3 uL 2% uranyl formate was added to grids adsorbed with 3uL protein sample, then blotted and air-dried. |
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Grid | Details: 400-Cu copper mesh with thin nitrocellulose support and thin carbon, glow discharged |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Temperature | Average: 298 K |
Alignment procedure | Legacy - Astigmatism: Objective astigmatism was corrected at 100,000 time magnification using a live feed of the power spectrum. |
Date | Jan 15, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 491 Details: 36 images were collected at each angle in 5 degree intervals from 0 degrees to -55 degrees. |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -1.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle min: -55 |
Experimental equipment | ![]() Model: Tecnai Spirit / Image courtesy: FEI Company |
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Image processing
Details | Particles were selected using automatic (difference-of-Gaussians) picking followed by reference-free classification to eliminate noisy picks or non-target aggregation states. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.3 Å / Resolution method: OTHER / Software - Name: Appion, spider, EMAN1, Xmipp / Number images used: 20917 |
Final two d classification | Number classes: 13 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: H / Chain - #1 - Chain ID: L / Chain - #2 - Chain ID: M |
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Software | Name: ![]() |
Details | The crystal structure was docked to the EM volume using the fitting function in UCSF Chimera. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |