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- PDB-7s08: Crystal structure of Epstein-Barr virus gH/gL targeting antibody 770F7 -

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Basic information

Entry
Database: PDB / ID: 7s08
TitleCrystal structure of Epstein-Barr virus gH/gL targeting antibody 770F7
Components
  • 770F7 Fab Heavy chain
  • 770F7 Fab Light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / gH/gL / Epstein-Barr virus / herpesvirus
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsChen, W.-H. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1ZIAAI000978-13 United States
CitationJournal: Immunity / Year: 2022
Title: Epstein-Barr virus gH/gL has multiple sites of vulnerability for virus neutralization and fusion inhibition.
Authors: Chen, W.H. / Kim, J. / Bu, W. / Board, N.L. / Tsybovsky, Y. / Wang, Y. / Hostal, A. / Andrews, S.F. / Gillespie, R.A. / Choe, M. / Stephens, T. / Yang, E.S. / Pegu, A. / Peterson, C.E. / ...Authors: Chen, W.H. / Kim, J. / Bu, W. / Board, N.L. / Tsybovsky, Y. / Wang, Y. / Hostal, A. / Andrews, S.F. / Gillespie, R.A. / Choe, M. / Stephens, T. / Yang, E.S. / Pegu, A. / Peterson, C.E. / Fisher, B.E. / Mascola, J.R. / Pittaluga, S. / McDermott, A.B. / Kanekiyo, M. / Joyce, M.G. / Cohen, J.I.
History
DepositionAug 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 770F7 Fab Heavy chain
L: 770F7 Fab Light chain
A: 770F7 Fab Heavy chain
B: 770F7 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,08614
Polymers96,1654
Non-polymers92110
Water6,467359
1
H: 770F7 Fab Heavy chain
L: 770F7 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5437
Polymers48,0832
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-24 kcal/mol
Surface area19560 Å2
MethodPISA
2
A: 770F7 Fab Heavy chain
B: 770F7 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5437
Polymers48,0832
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-31 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.194, 40.222, 135.151
Angle α, β, γ (deg.)90.000, 110.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 770F7 Fab Heavy chain


Mass: 24684.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 770F7 Fab Light chain


Mass: 23397.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES PH7.5, 0.1M CaCl2, 25% PEG3350, 4% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22877 / % possible obs: 95.4 % / Redundancy: 4.5 % / CC1/2: 0.85 / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.5 Å / Num. unique obs: 1928 / CC1/2: 0.52

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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: 4QHK

4qhk


Resolution: 2.42→44.62 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 1997 5.52 %
Rwork0.2122 34170 -
obs0.2148 22877 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.74 Å2 / Biso mean: 36.976 Å2 / Biso min: 7.65 Å2
Refinement stepCycle: final / Resolution: 2.42→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6700 0 60 359 7119
Biso mean--43.45 38.32 -
Num. residues----881
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.42-2.480.41271200.3232054217484
2.48-2.550.33441380.28632355249396
2.55-2.620.28291400.27062392253299
2.62-2.710.3141460.254624802626100
2.71-2.810.3021420.248324362578100
2.81-2.920.271440.238124612605100
2.92-3.050.2871430.223124532596100
3.05-3.210.27841450.21224662611100
3.21-3.410.2671430.204124772620100
3.41-3.680.23391460.197124872633100
3.68-4.050.24691450.182724672612100
4.05-4.630.20431450.167324902635100
4.63-5.830.22261480.188425352683100
5.83-44.620.2731520.222826172769100
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)
13.137-0.5282-0.59662.04990.73524.35790.07610.19070.1898-0.1627-0.0643-0.10450.0970.15180.03250.1635-0.00350.01180.14590.03420.1784-10.46233.014141.466
25.3095-1.9609-2.39421.01982.50239.18490.02090.7920.2563-0.4664-0.3394-0.4638-0.61060.04420.27930.2927-0.0376-0.08710.3479-00.2479-11.76333.782129.953
33.58222.06650.55744.56321.21582.26480.1925-0.0674-0.33150.0256-0.18240.24520.2299-0.0927-0.01520.18310.0291-0.00190.13520.02070.3215-32.05911.467156.995
44.80073.14850.79229.78360.61293.0374-0.30910.30260.8365-0.33760.11840.8274-0.4659-0.33830.20250.28640.1109-0.06340.3920.01130.3403-33.64834.507126.513
55.30930.5704-0.29914.97560.82715.1513-0.01520.4447-0-0.3948-0.08830.06770.0663-0.36660.15090.17250.0171-0.01850.2611-0.0070.1524-26.48127.798124.083
61.81350.9995-1.06790.9307-0.80462.04860.08350.13270.1540.01790.03730.2917-0.0441-0.1859-0.09920.15670.06890.00940.2335-0.03250.3217-40.10221.277147.585
73.0775-0.1249-0.40561.55161.28195.80820.0507-0.1576-0.03-0.0764-0.01320.3693-0.2719-0.1157-0.07780.15240.024-0.00280.18080.04590.3656-42.85520.656154.685
82.8296-0.50861.12781.6352-0.5248.8895-0.0846-0.4683-0.17770.20150.22910.45310.2657-1.2471-0.21650.25240.00030.07330.39350.04910.4554-53.15316.955158.056
93.00840.6684-0.32282.77770.00924.127-0.0512-0.02220.0981-0.1601-0.0552-0.0141-0.06080.20460.11370.1985-0.01570.00790.1575-0.01870.1512.9278.981149.532
102.43910.2745-2.14010.4509-0.18054.9585-0.0145-0.1193-0.0317-0.03320.0634-0.2170.09980.5973-0.0120.24190.0201-0.02850.2771-0.03590.26959.0528.552152.111
111.8848-0.789-0.69341.5532-0.55420.8424-0.1298-0.40490.35650.4837-0.16270.1223-0.33840.08370.26850.3947-0.0118-0.01370.2043-0.01240.2189-7.40227.327179.287
123.63391.33790.94264.78141.4942.639-0.08520.03220.25050.3851-0.07470.0552-0.3142-0.0280.20610.3120.0088-0.01110.13220.02750.2272-4.92131.938175.42
134.15891.29520.75463.2817-0.70883.79490.01660.02630.0321-0.01870.1287-0.653-0.0690.7186-0.11170.1819-0.00930.02630.427-0.09620.342223.1911.73162.572
141.1543-1.4626-1.24952.5042.34754.67770.0686-0.08490.05480.04840.3097-0.58550.03150.8089-0.33580.205-0.02-0.04290.513-0.04170.333822.14314.091166.573
156.17851.0056-0.97592.1962-0.26393.0807-0.1314-0.3671-0.00240.4453-0.04060.07010.1695-0.00550.15010.37230.0077-0.01220.164-0.01010.24820.0124.149189.324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:97 )H1 - 97
2X-RAY DIFFRACTION2( CHAIN H AND RESID 98:121 )H98 - 121
3X-RAY DIFFRACTION3( CHAIN H AND RESID 122:226 )H122 - 226
4X-RAY DIFFRACTION4( CHAIN L AND RESID 1:30 )L1 - 30
5X-RAY DIFFRACTION5( CHAIN L AND RESID 31:91 )L31 - 91
6X-RAY DIFFRACTION6( CHAIN L AND RESID 92:151 )L92 - 151
7X-RAY DIFFRACTION7( CHAIN L AND RESID 152:188 )L152 - 188
8X-RAY DIFFRACTION8( CHAIN L AND RESID 189:214 )L189 - 214
9X-RAY DIFFRACTION9( CHAIN A AND RESID 1:82 )A1 - 82
10X-RAY DIFFRACTION10( CHAIN A AND RESID 83:121 )A83 - 121
11X-RAY DIFFRACTION11( CHAIN A AND RESID 122:146 )A122 - 146
12X-RAY DIFFRACTION12( CHAIN A AND RESID 147:226 )A147 - 226
13X-RAY DIFFRACTION13( CHAIN B AND RESID 1:62 )B1 - 62
14X-RAY DIFFRACTION14( CHAIN B AND RESID 63:114 )B63 - 114
15X-RAY DIFFRACTION15( CHAIN B AND RESID 115:215 )B115 - 215

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