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- PDB-8sgg: Crystal structure of Cy137D09, a monoclonal antibody isolated fro... -

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Basic information

Entry
Database: PDB / ID: 8sgg
TitleCrystal structure of Cy137D09, a monoclonal antibody isolated from macaques immunized with an Epstein-Barr virus glycoprotein 350 (gp350) nanoparticle vaccine
Components
  • Cy137D09 Fab heavy chain
  • Cy137D09 Fab light chain
KeywordsIMMUNE SYSTEM / monoclonal antibody / macaques / Epstein-Barr virus / antiviral
Biological speciesMacaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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-07-2-0067 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 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: Cy137D09 Fab heavy chain
B: Cy137D09 Fab light chain
C: Cy137D09 Fab heavy chain
D: Cy137D09 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,56412
Polymers95,8274
Non-polymers7378
Water7,080393
1
A: Cy137D09 Fab heavy chain
B: Cy137D09 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2826
Polymers47,9132
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-27 kcal/mol
Surface area20610 Å2
MethodPISA
2
C: Cy137D09 Fab heavy chain
D: Cy137D09 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2826
Polymers47,9132
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-28 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.794, 71.463, 86.451
Angle α, β, γ (deg.)90.00, 107.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Cy137D09 Fab heavy chain


Mass: 24604.676 Da / Num. of mol.: 2
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 Cy137D09 Fab light chain


Mass: 23308.805 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M calcium acetate, 0.1M sodium cacodylate pH 6.5, 17.5% w/v PEG 8000

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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: Feb 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 51917 / % possible obs: 85.7 % / Redundancy: 2.7 % / Rrim(I) all: 0.171 / Net I/σ(I): 9.4
Reflection shellResolution: 2.03→2.12 Å / Num. unique obs: 2870 / CC1/2: 0.642 / Rrim(I) all: 0.722

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8SGN

8sgn


Resolution: 2.03→36.12 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 30.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 1825 3.86 %
Rwork0.1905 --
obs0.1926 47334 78.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→36.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6658 0 48 393 7099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066881
X-RAY DIFFRACTIONf_angle_d0.8769367
X-RAY DIFFRACTIONf_dihedral_angle_d11.179958
X-RAY DIFFRACTIONf_chiral_restr0.0521059
X-RAY DIFFRACTIONf_plane_restr0.0051183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.3981560.29571420X-RAY DIFFRACTION32
2.08-2.140.3232750.28792193X-RAY DIFFRACTION49
2.14-2.210.30541260.2732934X-RAY DIFFRACTION66
2.21-2.290.33561320.25683354X-RAY DIFFRACTION75
2.29-2.380.33051520.24493565X-RAY DIFFRACTION80
2.38-2.490.3151500.23263703X-RAY DIFFRACTION83
2.49-2.620.26481540.23523804X-RAY DIFFRACTION86
2.62-2.790.31381670.22143939X-RAY DIFFRACTION89
2.79-30.26171580.20694037X-RAY DIFFRACTION90
3-3.30.24911600.19094108X-RAY DIFFRACTION91
3.3-3.780.23371590.17324180X-RAY DIFFRACTION93
3.78-4.760.19871680.14524163X-RAY DIFFRACTION92
4.76-36.120.18411680.1544109X-RAY DIFFRACTION89
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)
15.72971.4323-0.26972.3336-1.00276.8439-0.42260.3157-0.0421-0.3350.1873-0.35490.54960.14190.14930.2904-0.00660.06870.16530.03370.270912.51531.41122.405
20.70290.03780.94932.0538-0.49463.747-0.21760.41640.1486-0.86640.0201-0.0918-0.32870.04460.10960.61290.0312-0.01440.41380.10040.23596.31628.97712.305
30.69640.66210.95180.71280.82491.3022-0.19030.7829-0.035-0.82230.00430.0225-0.3845-0.0948-0.28560.66590.0520.03020.45880.05480.2146.72929.65711.88
42.91541.20030.7461.79021.16552.88080.10570.31620.0231-0.77930.1455-0.4336-0.35910.18310.14320.38940.07880.04530.17250.04970.217810.49824.75120.495
52.9044-2.03210.07463.18090.72210.8989-0.05860.14890.067-0.03350.0208-0.39070.19760.07940.01640.28250.0267-0.00420.18320.00430.243728.74717.87636.913
62.2962-0.10070.96413.29121.09013.61550.07490.4568-0.0734-0.7398-0.0702-0.0660.10730.21590.02080.57650.0997-0.00470.3963-0.03910.18563.1378.4699.37
73.61761.34993.05463.94723.57335.8815-0.1841-0.0306-0.1552-0.58940.03330.0114-0.47530.25580.11240.27710.0247-0.00160.13110.03430.16722.0916.09242.015
81.7386-0.0164-0.4123.6142-0.05557.1256-0.0926-0.0046-0.106-0.2207-0.0040.057-0.2175-0.05830.06220.1940.0217-0.01240.18160.02540.187920.0235.37246.101
94.501-0.1202-1.49613.87470.22436.46910.0352-0.23870.18150.55090.21230.36750.0051-0.1436-0.0940.2663-0.02880.04060.2025-0.05130.24851.18830.15967.314
103.84170.1893-1.013.2836-0.90423.9194-0.0586-0.28680.32470.3295-0.0115-0.0835-0.55070.07280.01210.3271-0.0198-0.02150.3107-0.03730.164511.46627.3369.335
115.5462.7498-3.38165.9636-6.17886.6050.0763-0.23381.15421.15981.0081.0035-2.1497-0.3971-0.07340.7177-0.1186-0.02810.6808-0.25520.19472.16336.06870.154
122.4043-0.49110.55423.018-0.24965.11510.0169-0.64840.16980.69110.22590.25490.2220.26270.16860.30980.01380.03530.3256-0.06040.12576.27423.09268.489
134.04631.6546-0.36062.2373-1.85371.7902-0.11160.4617-0.3553-0.06750.36790.24550.4402-0.2994-0.20280.2328-0.0423-0.01870.2146-0.02570.2708-16.59813.82640.367
144.36821.8275-0.10564.4974-0.00591.0392-0.1298-0.05930.12560.04740.03260.34070.0705-0.08010.07130.2673-0.0168-0.05320.19260.00090.1735-13.39318.80847.225
152.5849-0.26111.01682.7925-1.66333.9982-0.1026-0.5923-0.36770.45560.07010.09490.07080.218-0.08170.3291-0.0269-0.02930.38950.07680.184511.5276.4272.674
162.48-0.6942.47622.1857-1.90055.4946-0.0314-0.1042-0.11670.50250.00970.105-0.2471-0.43750.02820.26880.003-0.01340.1459-0.00230.1986-7.3866.0840.026
172.9432-0.01970.91135.0948-1.03677.2142-0.16590.0683-0.11990.09850.11410.0336-0.2764-0.02850.05930.17990.0268-0.01350.1979-0.03540.216-5.7085.55935.676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:17 )A1 - 17
2X-RAY DIFFRACTION2( CHAIN A AND RESID 18:65 )A18 - 65
3X-RAY DIFFRACTION3( CHAIN A AND RESID 66:113 )A66 - 113
4X-RAY DIFFRACTION4( CHAIN A AND RESID 114:132 )A114 - 132
5X-RAY DIFFRACTION5( CHAIN A AND RESID 133:214 )A133 - 214
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1:115 )B1 - 115
7X-RAY DIFFRACTION7( CHAIN B AND RESID 116:160 )B116 - 160
8X-RAY DIFFRACTION8( CHAIN B AND RESID 161:209 )B161 - 209
9X-RAY DIFFRACTION9( CHAIN C AND RESID 1:33 )C1 - 33
10X-RAY DIFFRACTION10( CHAIN C AND RESID 34:73 )C34 - 73
11X-RAY DIFFRACTION11( CHAIN C AND RESID 74:84 )C74 - 84
12X-RAY DIFFRACTION12( CHAIN C AND RESID 85:132 )C85 - 132
13X-RAY DIFFRACTION13( CHAIN C AND RESID 133:158 )C133 - 158
14X-RAY DIFFRACTION14( CHAIN C AND RESID 159:213 )C159 - 213
15X-RAY DIFFRACTION15( CHAIN D AND RESID 1:115 )D1 - 115
16X-RAY DIFFRACTION16( CHAIN D AND RESID 116:160 )D116 - 160
17X-RAY DIFFRACTION17( CHAIN D AND RESID 161:210 )D161 - 210

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