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- PDB-8sef: Crystal structure of Cy137C02, a monoclonal antibody isolated fro... -

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Basic information

Entry
Database: PDB / ID: 8sef
TitleCrystal structure of Cy137C02, a monoclonal antibody isolated from macaques immunized with an Epstein-Barr virus glycoprotein 350 (gp350) nanoparticle vaccine
Components
  • Cy137C02 Fab heavy chain
  • Cy137C02 Fab light chain
KeywordsIMMUNE SYSTEM / monoclonal antibody / antiviral / Epstein-Barr virus
Biological speciesMacaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsJoyce, M.G. / Jensen, J.L. / Chen, W.H. / Kanekiyo, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-18-2-0040 United States
CitationJournal: Immunity / Year: 2025
Title: Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350.
Authors: Joyce, M.G. / Bu, W. / Chen, W.H. / Gillespie, R.A. / Andrews, S.F. / Wheatley, A.K. / Tsybovsky, Y. / Jensen, J.L. / Stephens, T. / Prabhakaran, M. / Fisher, B.E. / Narpala, S.R. / Bagchi, ...Authors: Joyce, M.G. / Bu, W. / Chen, W.H. / Gillespie, R.A. / Andrews, S.F. / Wheatley, A.K. / Tsybovsky, Y. / Jensen, J.L. / Stephens, T. / Prabhakaran, M. / Fisher, B.E. / Narpala, S.R. / Bagchi, M. / McDermott, A.B. / Nabel, G.J. / Kwong, P.D. / Mascola, J.R. / Cohen, J.I. / Kanekiyo, M.
History
DepositionApr 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Feb 19, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Feb 26, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Cy137C02 Fab heavy chain
L: Cy137C02 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,45610
Polymers46,7152
Non-polymers7418
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-44 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.389, 67.125, 50.244
Angle α, β, γ (deg.)90.00, 106.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-409-

HOH

21H-415-

HOH

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Components

#1: Antibody Cy137C02 Fab heavy chain


Mass: 23908.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody Cy137C02 Fab light chain


Mass: 22806.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1x PBS, Cryoprotectant: 3M ammonium sulfate, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 16004 / % possible obs: 95.2 % / Redundancy: 2.9 % / Rrim(I) all: 0.132 / Net I/σ(I): 11.1
Reflection shellResolution: 2.47→2.56 Å / Num. unique obs: 1453 / CC1/2: 0.759

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8SIC

8sic


Resolution: 2.47→38.27 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 29.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 1522 10 %
Rwork0.2224 --
obs0.2266 15222 90.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.47→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 47 23 3358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023443
X-RAY DIFFRACTIONf_angle_d0.624692
X-RAY DIFFRACTIONf_dihedral_angle_d15.8321229
X-RAY DIFFRACTIONf_chiral_restr0.046524
X-RAY DIFFRACTIONf_plane_restr0.005592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.550.35441090.2967956X-RAY DIFFRACTION71
2.55-2.640.35991340.29211140X-RAY DIFFRACTION84
2.64-2.740.33551330.29661205X-RAY DIFFRACTION88
2.75-2.870.32131340.26641224X-RAY DIFFRACTION89
2.87-3.020.31131360.24741264X-RAY DIFFRACTION93
3.02-3.210.28891510.25741312X-RAY DIFFRACTION95
3.21-3.460.27531450.23741297X-RAY DIFFRACTION94
3.46-3.810.25171400.23031345X-RAY DIFFRACTION96
3.81-4.350.26661450.18911312X-RAY DIFFRACTION96
4.36-5.480.22131440.18211324X-RAY DIFFRACTION95
5.49-38.270.24241510.22021321X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8127-0.398-0.91063.3539-0.47234.2990.01-0.24130.24540.19980.17690.30140.38-0.2867-0.23930.4327-0.032-0.00060.4087-0.00670.4238-22.534-8.08130.128
21.88970.24461.05331.38920.50072.9794-0.0552-0.1757-0.09360.19910.1067-0.04270.388-0.3186-0.08390.4766-0.01370.04760.38760.10010.4112-26.916-17.56920.03
35.44632.4567-0.79825.4835-0.01533.15610.0023-0.44520.0391-0.0462-0.18640.45650.3462-0.26410.150.3714-0.0109-0.01510.41650.02890.4417-39.04-20.8935.74
43.12140.4683-0.21142.74741.37852.49670.5349-0.5044-0.50340.5606-0.104-0.22120.64470.2023-0.3980.9403-0.0741-0.15610.60990.11050.578-17.714-32.99234.196
52.35780.60442.35321.97560.03763.84830.2139-0.3636-0.260.20660.0286-0.22260.3428-0.5302-0.1430.37720.08730.11440.4281-0.00990.432-23.122-27.20715.161
63.41540.31290.58546.5848-1.52013.6185-0.0021-0.0058-0.0478-0.4394-0.0147-0.27980.32060.0168-0.00020.41760.00880.02680.3785-0.04520.3702-28.352-31.863-4.382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:83 )H1 - 83
2X-RAY DIFFRACTION2( CHAIN H AND RESID 84:141 )H84 - 141
3X-RAY DIFFRACTION3( CHAIN H AND RESID 142:216 )H142 - 216
4X-RAY DIFFRACTION4( CHAIN L AND RESID 1:86 )L1 - 86
5X-RAY DIFFRACTION5( CHAIN L AND RESID 87:135 )L87 - 135
6X-RAY DIFFRACTION6( CHAIN L AND RESID 136:210 )L136 - 210

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