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- PDB-8sga: Crystal structure of 770E11, a monoclonal antibody isolated from ... -

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Basic information

Entry
Database: PDB / ID: 8sga
TitleCrystal structure of 770E11, a monoclonal antibody isolated from a human Epstein-Barr virus seropositive donor
Components
  • 770E11 Fab heavy chain
  • 770E11 Fab light chain
KeywordsIMMUNE SYSTEM / monoclonal antibody / Epstein-Barr virus / human protein
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, W.H. / Jensen, J.L. / Joyce, M.G.
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 1.1Oct 30, 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
L: 770E11 Fab light chain
H: 770E11 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6974
Polymers46,0182
Non-polymers6792
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-18 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.140, 73.080, 132.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 770E11 Fab light chain


Mass: 22199.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 770E11 Fab heavy chain


Mass: 23818.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: 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.: 1
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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2M ammonium sulfate, 2% w/v PEG 400, 0.1M sodium acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 28509 / % possible obs: 85.9 % / Redundancy: 3.7 % / CC1/2: 0.909 / Net I/σ(I): 6.14
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 2886 / CC1/2: 0.458

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→36.51 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 1422 5 %
Rwork0.2056 --
obs-28415 85.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 6 331 3551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093278
X-RAY DIFFRACTIONf_angle_d1.0334473
X-RAY DIFFRACTIONf_dihedral_angle_d13.744464
X-RAY DIFFRACTIONf_chiral_restr0.066509
X-RAY DIFFRACTIONf_plane_restr0.007570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.29371220.26212410X-RAY DIFFRACTION69
1.94-1.980.29941420.25612665X-RAY DIFFRACTION77
1.98-2.020.26131550.25132792X-RAY DIFFRACTION79
2.02-2.080.30331410.24262752X-RAY DIFFRACTION79
2.08-2.130.25661430.23422764X-RAY DIFFRACTION80
2.13-2.190.27881490.24092855X-RAY DIFFRACTION81
2.19-2.270.24521470.22122777X-RAY DIFFRACTION80
2.27-2.350.27991500.22562850X-RAY DIFFRACTION80
2.35-2.440.231380.21922761X-RAY DIFFRACTION79
2.44-2.550.27011450.21012779X-RAY DIFFRACTION80
2.55-2.690.28251470.20682737X-RAY DIFFRACTION79
2.69-2.850.24941420.20142778X-RAY DIFFRACTION78
2.85-3.070.24141400.18912702X-RAY DIFFRACTION78
3.07-3.380.22471410.17562725X-RAY DIFFRACTION78
3.38-3.870.22321370.17062695X-RAY DIFFRACTION77
3.87-4.880.17411450.15242635X-RAY DIFFRACTION76
4.88-36.510.25681310.21842614X-RAY DIFFRACTION75
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)
12.0927-0.12060.1961.4330.16491.63040.0332-0.22410.37110.2809-0.0682-0.0785-0.76320.12810.03060.3701-0.0838-0.03220.148-0.04650.1392.0411.04-2.606
22.50720.29660.71352.61560.27882.8794-0.007-0.03240.00480.11520.05960.0622-0.2151-0.0489-0.04870.1190.01290.02710.03960.02320.0851-26.30516.101-29.152
31.4006-0.73650.69880.8290.24311.68170.03730.2569-0.0986-0.06350.0156-0.038-0.05170.1809-0.0650.064-0.00690.00120.12540.01660.1451-4.095-12.307-13.98
43.2835-0.5267-0.70432.46610.80442.16510.0016-0.04170.21370.11110.07680.2123-0.15140.0201-0.04050.0432-0.0196-0.00110.07930.04090.0884-3.39-4.682-5.407
51.67750.27260.37721.1615-0.67981.1950.0055-0.2003-0.27040.1252-0.0016-0.09910.11360.0703-0.00520.05360.01230.00410.12050.04780.1211-5.212-12.144-5.444
64.1104-0.54090.10873.0616-0.69342.59050.21180.0534-0.11760.09190.0633-0.2771-0.02960.5276-0.14360.0962-0.0421-0.02340.17950.01980.17455.534-2.68-5.545
70.89620.0110.47112.3296-0.73671.5547-0.0503-0.02760.0121-0.43590.0911-0.0551-0.0091-0.0878-0.1631-0.0246-0.00020.00980.07570.03130.0991-20.8220.752-28.585
81.38530.3304-0.30072.0208-0.7442.37940.05020.01680.09110.07050.1841-0.2628-0.26420.129-0.11390.0906-0.03720.02490.07070.00710.1483-15.7655.007-29.285
92.01490.6759-1.25823.6764-2.44154.83510.10380.2148-0.1398-0.494-0.0022-0.0460.25960.15560.07480.1691-0.0194-0.00880.0687-0.02850.1279-14.784-0.891-37.354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN L AND RESID 2:110 )L2 - 110
2X-RAY DIFFRACTION2( CHAIN L AND RESID 111:208 )L111 - 208
3X-RAY DIFFRACTION3( CHAIN H AND RESID 1:33 )H1 - 33
4X-RAY DIFFRACTION4( CHAIN H AND RESID 34:54 )H34 - 54
5X-RAY DIFFRACTION5( CHAIN H AND RESID 55:101 )H55 - 101
6X-RAY DIFFRACTION6( CHAIN H AND RESID 102:116 )H102 - 116
7X-RAY DIFFRACTION7( CHAIN H AND RESID 117:155 )H117 - 155
8X-RAY DIFFRACTION8( CHAIN H AND RESID 156:198 )H156 - 198
9X-RAY DIFFRACTION9( CHAIN H AND RESID 199:214 )H199 - 214

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