[English] 日本語
Yorodumi
- EMDB-5834: A Unique Human Mycoplasma Protein that Generically Blocks Antigen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5834
TitleA Unique Human Mycoplasma Protein that Generically Blocks Antigen-Antibody Union
Map dataProtein M and Fab b12
Sample
  • Sample: Fab of human mAb b12 in complex with Full length MG281
  • Protein or peptide: MG281
  • Protein or peptide: mAb b12 Fab
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) / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 21.3 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.49
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.49
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5834.gif

Downloads & links

-
Map

FileDownload / File: emd_5834.map.gz / Format: CCP4 / Size: 670.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProtein M and Fab b12
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 56 pix.
= 114.8 Å		2.05 Å/pix.
x 56 pix.
= 114.8 Å		2.05 Å/pix.
x 56 pix.
= 114.8 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: 1.49 / Movie #1: 1.49
Minimum - Maximum-2.33756256 - 9.292819980000001
Average (Standard dev.)-0.0000576 (±0.88106066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-11-11-11
Dimensions565656
Spacing565656
CellA=B=C: 114.799995 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z565656
origin x/y/z0.0000.0000.000
length x/y/z114.800114.800114.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-11-11-11
NC/NR/NS565656
D min/max/mean-2.3389.293-0.000

-
Supplemental data

-
Sample components

-
Entire : Fab of human mAb b12 in complex with Full length MG281

EntireName: Fab of human mAb b12 in complex with Full length MG281
Components
  • Sample: Fab of human mAb b12 in complex with Full length MG281
  • Protein or peptide: MG281
  • Protein or peptide: mAb b12 Fab

-
Supramolecule #1000: Fab of human mAb b12 in complex with Full length MG281

SupramoleculeName: 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
Molecular weightTheoretical: 100 KDa / Method: Western blot

-
Macromolecule #1: MG281

MacromoleculeName: MG281 / 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

-
Macromolecule #2: mAb b12 Fab

MacromoleculeName: mAb b12 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
TemperatureAverage: 298 K
Alignment procedureLegacy - Astigmatism: Objective astigmatism was corrected at 100,000 time magnification using a live feed of the power spectrum.
DateJan 15, 2013
Image recordingCategory: 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 max0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -1.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle min: -55
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

-
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: 21.3 Å / Resolution method: OTHER / Software - Name: Appion, spider, EMAN1, Xmipp / Number images used: 20917
Final two d classificationNumber classes: 13

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more