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

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Basic information

Entry
Database: PDB / ID: 8fxy
TitleCryo-EM structure of cowpox virus M2 in complex with human B7.2 (hexameric ring)
Components
  • CPXV040 protein
  • T-lymphocyte activation antigen CD86
KeywordsVIRAL PROTEIN / poxvirus M2 protein / OPG038 / T-cell costimulation / poxviral immune evasion domain PIE / B7.2 / Structural Genomics / CSGID
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 / adaptive immune response / symbiont-mediated suppression of host NF-kappaB cascade / 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 speciesCowpox virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsElliott, J.I. / Adams, L.J. / Nelson, C.A. / Fremont, D.H. / CSBID
Funding support United States, 1items
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, J.I. / Adams, L.J. / Jethva, P.N. / Gross, M.L. / Nelson, C.A. / Fremont, D.H.
History
DepositionJan 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Data collection / Structure summary / Category: audit_author / em_admin / Item: _em_admin.last_update
Revision 1.1Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CPXV040 protein
H: T-lymphocyte activation antigen CD86
B: CPXV040 protein
C: T-lymphocyte activation antigen CD86
D: CPXV040 protein
E: T-lymphocyte activation antigen CD86
F: CPXV040 protein
G: T-lymphocyte activation antigen CD86
I: CPXV040 protein
J: T-lymphocyte activation antigen CD86
K: CPXV040 protein
L: T-lymphocyte activation antigen CD86
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,85530
Polymers290,87312
Non-polymers3,98218
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
CPXV040 protein


Mass: 23396.398 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpox virus (Brighton Red) / Gene: CPXV040 CDS / Cell (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q8QN22
#2: Protein
T-lymphocyte activation antigen CD86 / Activation B7-2 antigen / B70 / BU63 / CTLA-4 counter-receptor B7.2 / FUN-1


Mass: 25082.463 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD86, CD28LG2 / Production host: Homo sapiens (human) / References: UniProt: P42081
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of 6 member ring-like M2 oligomers bound to B7.2 ectodomans
Type: COMPLEX / Entity ID: #2 / Source: MULTIPLE SOURCES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Cowpox virus (Brighton Red)265872
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4 / Details: 150 mM Nacl, 25 mM HEPES, pH7.4
Buffer component
IDConc.NameFormulaBuffer-ID
18.7 g/Lsodium chlorideNaCl1
26.0 g/LHEPESHEPES1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 66 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategoryDetails
7UCSF ChimeraX1.3model fittingfit to map
9PHENIX1.20.1-4487model refinementreal space refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75929 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215360
ELECTRON MICROSCOPYf_angle_d0.47920790
ELECTRON MICROSCOPYf_dihedral_angle_d10.365670
ELECTRON MICROSCOPYf_chiral_restr0.042346
ELECTRON MICROSCOPYf_plane_restr0.0032640

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