[English] 日本語
Yorodumi
- EMDB-35074: Cryo-EM structure of MPXV M2 in complex with human B7.1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35074
TitleCryo-EM structure of MPXV M2 in complex with human B7.1
Map data
Sample
  • Complex: M2-hB7.1
    • Protein or peptide: NFkB inhibitor
    • Protein or peptide: T-lymphocyte activation antigen CD80
KeywordsM2 / complex / immune evasion / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of T cell mediated immunity / positive regulation of T-helper 1 cell differentiation / protein complex involved in cell adhesion / positive regulation of signal transduction / CD28 co-stimulation / positive regulation of granulocyte macrophage colony-stimulating factor production / CD28 dependent Vav1 pathway / CTLA4 inhibitory signaling / Interleukin-10 signaling / CD28 dependent PI3K/Akt signaling ...negative regulation of T cell mediated immunity / positive regulation of T-helper 1 cell differentiation / protein complex involved in cell adhesion / positive regulation of signal transduction / CD28 co-stimulation / positive regulation of granulocyte macrophage colony-stimulating factor production / CD28 dependent Vav1 pathway / CTLA4 inhibitory signaling / Interleukin-10 signaling / CD28 dependent PI3K/Akt signaling / coreceptor activity / positive regulation of T cell proliferation / T cell costimulation / positive regulation of interleukin-2 production / T cell activation / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / PIP3 activates AKT signaling / virus receptor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cellular response to lipopolysaccharide / cell surface receptor signaling pathway / intracellular signal transduction / receptor ligand activity / immune response / external side of plasma membrane / positive regulation of DNA-templated transcription / cell surface / plasma membrane
Similarity search - Function
Poxvirus M2 / CD80, IgC-like domain / CD80, immunoglobulin variable domain / Poxvirus M2 protein / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Poxvirus M2 / CD80, IgC-like domain / CD80, immunoglobulin variable domain / Poxvirus M2 protein / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-lymphocyte activation antigen CD80 / Early protein OPG038
Similarity search - Component
Biological speciesHomo sapiens (human) / Monkeypox virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsWang Y / Yang S / Zhao H / Deng Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Structural and functional insights into the modulation of T cell costimulation by monkeypox virus protein M2.
Authors: Shangyu Yang / Yong Wang / Feiyang Yu / Rao Cheng / Yiwei Zhang / Dan Zhou / Xuanxiu Ren / Zengqin Deng / Haiyan Zhao /
Abstract: The rapid spread of monkeypox in multiple countries has resulted in a global public health threat and has caused international concerns since May 2022. Poxvirus encoded M2 protein is a member of the ...The rapid spread of monkeypox in multiple countries has resulted in a global public health threat and has caused international concerns since May 2022. Poxvirus encoded M2 protein is a member of the poxvirus immune evasion family and plays roles in host immunomodulation via the regulation of innate immune response mediated by the NF-κB pathway and adaptive immune response mediated by B7 ligands. However, the interaction of monkeypox virus (MPXV) M2 with B7 ligands and structural insight into poxviral M2 function have remained elusive. Here we reveal that MPXV M2, co-existing as a hexamer and a heptamer, recognizes human B7.1 and B7.2 (hB7.1/2) with high avidities. The binding of oligomeric MPXV M2 interrupts the interactions of hB7.1/2 with CD28 and CTLA4 and subverts T cell activation mediated by B7.1/2 costimulatory signals. Cryo-EM structures of M2 in complex with hB7.1/2 show that M2 binds to the shallow concave face of hB7.1/2 and displays sterically competition with CD28 and CTLA4 for the binding to hB7.1/2. Our findings provide structural mechanisms of poxviral M2 function and immune evasion deployed by poxviruses.
History
DepositionJan 4, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35074.png

Downloads & links

-
Map

FileDownload / File: emd_35074.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 320 pix.
= 304. Å		0.95 Å/pix.
x 320 pix.
= 304. Å		0.95 Å/pix.
x 320 pix.
= 304. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.3808984 - 2.1903286
Average (Standard dev.)0.0008295448 (±0.041981842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 304.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_35074_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_35074_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : M2-hB7.1

EntireName: M2-hB7.1
Components
  • Complex: M2-hB7.1
    • Protein or peptide: NFkB inhibitor
    • Protein or peptide: T-lymphocyte activation antigen CD80

-
Supramolecule #1: M2-hB7.1

SupramoleculeName: M2-hB7.1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: NFkB inhibitor

MacromoleculeName: NFkB inhibitor / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Monkeypox virus
Molecular weightTheoretical: 23.285348 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VEYKNTICPP RQDYRYWYFV AELTIGVNYD INSTIIGECH MSESYIDRNA NIVLTGYGLK INMTIMDTDQ RFVAAAEGVG KDNKLSVLL FTTQRLDKVH HNISVTITCM EMNCGTTKYN SDLPESIHKS SSCDITINGS CVTCVNLETD PTKINPHYLH P KNKYLYHN ...String:
VEYKNTICPP RQDYRYWYFV AELTIGVNYD INSTIIGECH MSESYIDRNA NIVLTGYGLK INMTIMDTDQ RFVAAAEGVG KDNKLSVLL FTTQRLDKVH HNISVTITCM EMNCGTTKYN SDLPESIHKS SSCDITINGS CVTCVNLETD PTKINPHYLH P KNKYLYHN SEYSMRGSYG VTFIDELNQC LLDIKELSYD ICYRE

UniProtKB: Early protein OPG038

-
Macromolecule #2: T-lymphocyte activation antigen CD80

MacromoleculeName: T-lymphocyte activation antigen CD80 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.893967 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VIHVTKEVKE VATLSCGHNV SVEELAQTRI YWQKEKKMVL TMMSGDMNIW PEYKNRTIFD ITNNLSIVIL ALRPSDEGTY ECVVLKYEK DAFKREHLAE VTLSVKADFP TPSISDFEIP TSNIRRIICS TSGGFPEPHL SWLENGEELN AINTTVSQDP E TELYAVSS ...String:
VIHVTKEVKE VATLSCGHNV SVEELAQTRI YWQKEKKMVL TMMSGDMNIW PEYKNRTIFD ITNNLSIVIL ALRPSDEGTY ECVVLKYEK DAFKREHLAE VTLSVKADFP TPSISDFEIP TSNIRRIICS TSGGFPEPHL SWLENGEELN AINTTVSQDP E TELYAVSS KLDFNMTTNH SFMCLIKYGH LRVNQTFNWN TT

UniProtKB: T-lymphocyte activation antigen CD80

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 251261
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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