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- EMDB-29548: Cryo-EM structure of cowpox virus M2 in complex with human B7.2 (... -

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Basic information

Entry
Database: EMDB / ID: EMD-29548
TitleCryo-EM structure of cowpox virus M2 in complex with human B7.2 (hexameric ring)
Map dataHEX M2 with B7.2
Sample
  • Complex: Complex of 6 member ring-like M2 oligomers bound to B7.2 ectodomans
    • Protein or peptide: T-lymphocyte activation antigen CD86
  • Protein or peptide: CPXV040 protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordspoxvirus M2 protein / OPG038 / T-cell costimulation / poxviral immune evasion domain PIE / B7.2 / Structural Genomics / CSGID / VIRAL PROTEIN
Function / homology
Function and homology information


positive regulation of lymphotoxin A production / positive regulation of T-helper 2 cell differentiation / Co-stimulation by CD28 / CD28 dependent Vav1 pathway / positive regulation of immunoglobulin production / host cell endoplasmic reticulum / Co-inhibition by CTLA4 / positive regulation of interleukin-4 production / Interleukin-10 signaling / B cell activation ...positive regulation of lymphotoxin A production / positive regulation of T-helper 2 cell differentiation / Co-stimulation by CD28 / CD28 dependent Vav1 pathway / positive regulation of immunoglobulin production / host cell endoplasmic reticulum / Co-inhibition by CTLA4 / positive regulation of interleukin-4 production / Interleukin-10 signaling / B cell activation / CD28 dependent PI3K/Akt signaling / coreceptor activity / negative regulation of T cell proliferation / T cell costimulation / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / T cell activation / positive regulation of non-canonical NF-kappaB signal transduction / centriolar satellite / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / signaling receptor activity / cellular response to lipopolysaccharide / virus receptor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / symbiont-mediated suppression of host NF-kappaB cascade / adaptive immune response / cell surface receptor signaling pathway / immune response / receptor ligand activity / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / cell surface / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
CD86, IgV domain / Poxvirus M2 / Poxvirus M2 protein / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...CD86, IgV domain / Poxvirus M2 / Poxvirus M2 protein / : / Immunoglobulin V-Type / 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 CD86 / Early protein OPG038
Similarity search - Component
Biological speciesHomo sapiens (human) / Cowpox virus (Brighton Red)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsElliott JI / Adams LJ / Nelson CA / Fremont DH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Structure basis of poxvirus mediated sabotage of T-cell costimulation
Authors: Elliott JI / Adams LJ / Jethva PN / Gross ML / Nelson CA / Fremont DH
History
DepositionJan 25, 2023-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29548.png

Downloads & links

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Map

FileDownload / File: emd_29548.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHEX M2 with B7.2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.017325995 - 1.8501046
Average (Standard dev.)0.0013657963 (±0.024592368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_29548_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_29548_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of 6 member ring-like M2 oligomers bound to B7.2 ectodomans

EntireName: Complex of 6 member ring-like M2 oligomers bound to B7.2 ectodomans
Components
  • Complex: Complex of 6 member ring-like M2 oligomers bound to B7.2 ectodomans
    • Protein or peptide: T-lymphocyte activation antigen CD86
  • Protein or peptide: CPXV040 protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of 6 member ring-like M2 oligomers bound to B7.2 ectodomans

SupramoleculeName: Complex of 6 member ring-like M2 oligomers bound to B7.2 ectodomans
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CPXV040 protein

MacromoleculeName: CPXV040 protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Cowpox virus (Brighton Red)
Molecular weightTheoretical: 23.396398 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KPEAEYKNTI CPPRQDYRYW YFAAELTIGV NYDINSTIMG ECHMSESYID RNANIVLTGY GLEINMTIMD TDQRFVAAAE GVGKDNKLS VLLFTTQRLD KVHHNISVTI TCMEMNCGTT KYDSDLPESI HHKSSCDITI NGSCVTCVNL ETDPTKINPH Y LHPKDKYL ...String:
KPEAEYKNTI CPPRQDYRYW YFAAELTIGV NYDINSTIMG ECHMSESYID RNANIVLTGY GLEINMTIMD TDQRFVAAAE GVGKDNKLS VLLFTTQRLD KVHHNISVTI TCMEMNCGTT KYDSDLPESI HHKSSCDITI NGSCVTCVNL ETDPTKINPH Y LHPKDKYL YRNSEYGMRG SYGVTFMDEL NQCFLDIKEV SYDICY

UniProtKB: Early protein OPG038

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Macromolecule #2: T-lymphocyte activation antigen CD86

MacromoleculeName: T-lymphocyte activation antigen CD86 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.082463 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLKIQAYFNE TADLPCQFAN SQNQSLSELV VFWQDQENLV LNEVYLGKEK FDSVHSKYMG RTSFDSDSWT LRLHNLQIKD KGLYQCIIH HKKPTGMIRI HQMNSELSVL ANFSQPEIVP ISNITENVYI NLTCSSIHGY PEPKKMSVLL RTKNSTIEYD G IMQKSQDN ...String:
MLKIQAYFNE TADLPCQFAN SQNQSLSELV VFWQDQENLV LNEVYLGKEK FDSVHSKYMG RTSFDSDSWT LRLHNLQIKD KGLYQCIIH HKKPTGMIRI HQMNSELSVL ANFSQPEIVP ISNITENVYI NLTCSSIHGY PEPKKMSVLL RTKNSTIEYD G IMQKSQDN VTELYDVSIS LSVSFPDVTS NMTIFCILET DKTRLLSSPF SIELEDPQPP P

UniProtKB: T-lymphocyte activation antigen CD86

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
8.7 g/LNaClsodium chloride
6.0 g/LHEPESHEPES

Details: 150 mM Nacl, 25 mM HEPES, pH7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5yxk

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75929
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8fxy:
Cryo-EM structure of cowpox virus M2 in complex with human B7.2 (hexameric ring)

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