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- PDB-8fxw: Cryo-EM structure of cowpox virus M2 in complex with human B7.1 (... -

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Basic information

Entry
Database: PDB / ID: 8fxw
TitleCryo-EM structure of cowpox virus M2 in complex with human B7.1 (hexameric ring)
Components
  • CPXV040 protein
  • T-lymphocyte activation antigen CD80
KeywordsVIRAL PROTEIN / poxvirus M2 protein / OPG038 / T-cell costimulation / poxviral immune evasion domain PIE / B7.1 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 / Co-stimulation by CD28 / positive regulation of granulocyte macrophage colony-stimulating factor production / CD28 dependent Vav1 pathway / positive regulation of peptidyl-tyrosine phosphorylation / host cell endoplasmic reticulum / Co-inhibition by CTLA4 ...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 / Co-stimulation by CD28 / positive regulation of granulocyte macrophage colony-stimulating factor production / CD28 dependent Vav1 pathway / positive regulation of peptidyl-tyrosine phosphorylation / host cell endoplasmic reticulum / Co-inhibition by CTLA4 / Interleukin-10 signaling / 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 / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / cellular response to lipopolysaccharide / virus receptor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / symbiont-mediated suppression of host NF-kappaB cascade / cell surface receptor signaling pathway / intracellular signal transduction / immune response / receptor ligand activity / external side of plasma membrane / positive regulation of DNA-templated transcription / cell surface / extracellular region / plasma membrane
Similarity search - Function
CD80, IgC-like domain / CD80, immunoglobulin variable domain / Poxvirus M2 / Poxvirus M2 protein / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...CD80, IgC-like domain / CD80, immunoglobulin variable domain / Poxvirus M2 / 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 speciesCowpox virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsElliott, J.I. / Adams, L.J. / Nelson, C.A. / Fremont, D.H. / CSBID / Center for Structural Genomics of Infectious Diseases (CSGID)
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 CD80
B: CPXV040 protein
C: T-lymphocyte activation antigen CD80
D: CPXV040 protein
E: T-lymphocyte activation antigen CD80
F: CPXV040 protein
G: T-lymphocyte activation antigen CD80
I: CPXV040 protein
J: T-lymphocyte activation antigen CD80
K: CPXV040 protein
L: T-lymphocyte activation antigen CD80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,80030
Polymers292,81812
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: 25809.906 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpox virus (Brighton Red) / Gene: CPXV040 CDS / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q8QN22
#2: Protein
T-lymphocyte activation antigen CD80 / Activation B7-1 antigen / BB1 / CTLA-4 counter-receptor B7.1 / B7


Mass: 22993.123 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD80, CD28LG, CD28LG1, LAB7 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P33681
#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: obtained synthetically / 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 M2 ring-like oligomers bound to B7.1 ectodomans
Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Cowpox virus (Brighton Red)265872
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293F
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

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 674730 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 56.41 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002515438
ELECTRON MICROSCOPYf_angle_d0.44820904
ELECTRON MICROSCOPYf_chiral_restr0.04382400
ELECTRON MICROSCOPYf_plane_restr0.00232628
ELECTRON MICROSCOPYf_dihedral_angle_d10.50985742

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