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- PDB-9oal: Cryo-EM structure of EBV gB prefusion construct C3-GT -

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Basic information

Entry
Database: PDB / ID: 9oal
TitleCryo-EM structure of EBV gB prefusion construct C3-GT
ComponentsEnvelope glycoprotein B
KeywordsVIRAL PROTEIN / fusion protein / engineered protein / stabilized protein / prefusion protein / gB / glycoprotein B
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
: / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological specieshuman gammaherpesvirus 4 (Epstein-Barr virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMcCool, R.S. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Design, Structure, and Immunogenicity of a Soluble Prefusion-stabilized EBV gB Antigen.
Authors: McCool, R.S. / Acreman, C.A. / Powell, A.E. / Picucci, S.I. / Stieh, D.J. / Huynh, J. / Caruso, H. / Park, S. / Chen, J.-L. / O'Rear, J. / Palanski, B.A. / Byrne, P.O. / Sponholtz, M.R. / ...Authors: McCool, R.S. / Acreman, C.A. / Powell, A.E. / Picucci, S.I. / Stieh, D.J. / Huynh, J. / Caruso, H. / Park, S. / Chen, J.-L. / O'Rear, J. / Palanski, B.A. / Byrne, P.O. / Sponholtz, M.R. / Chou, C.-W. / Ledgerwood, J.E. / Weidenbacher, P.A.-B. / McLellan, J.S.
History
DepositionApr 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein B
B: Envelope glycoprotein B
C: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,6796
Polymers257,9203
Non-polymers1,7603
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Envelope glycoprotein B / gB


Mass: 85973.250 Da / Num. of mol.: 3
Mutation: I89C, W112H, Y113R, W193R, L194V, I195E, W196A, A175C, D220E, H316I, D320Q, S325L, R428G, R429G, R439S, R431G, R432G, L628GCG, E634C
Source method: isolated from a genetically manipulated source
Details: C-terminally truncated recombinant ectodomain construct
Source: (gene. exp.) human gammaherpesvirus 4 (Epstein-Barr virus)
Strain: M81 / Gene: gB, BALF4 / Cell line (production host): Hek293F / Production host: Homo sapiens (human) / References: UniProt: P0C762
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
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: Prefusion-stabilized Epstein-Barr virus glycoprotein B
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.251 MDa / Experimental value: NO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus) / Strain: M81
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Details: 2 mM Tris (pH 8.0), 200 mM NaCl, 2 mM CaCl2, and 0.02% (w/v) sodium azide (SEC buffer). CHAPS was added immediately before freezing to a final concentration of 2 mM (0.25x CMC or 0.123% w/v).
Buffer component
IDConc.NameFormulaBuffer-ID
12 mMTris base1
2200 mMsodium chlorideNaCl1
32 mMcalcium chlorideCaCl21
40.02 % (w/v)sodium azideNaN31
51
SpecimenConc.: 6.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4541

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7PHENIXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13Cootmodel refinement
14ISOLDEmodel refinement
Image processingDetails: Prefusion stabilized Epstein-Barr virus envelope glycoprotein B
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2178814
Details: Particle picking was performed initially using blob picker. After initial, on-the-fly processing in CryoSparc Live, templates were generated for subsequent template-based picking.
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162928 / Symmetry type: POINT
Atomic model buildingDetails: Template-based, PDB: 7KDP / Source name: AlphaFold / Type: in silico model

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