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- PDB-7ps3: Crystal structure of antibody Beta-32 Fab -

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Basic information

Entry
Database: PDB / ID: 7ps3
TitleCrystal structure of antibody Beta-32 Fab
Components
  • Beta-32 heavy chain
  • Beta-32 light chain
KeywordsVIRAL PROTEIN / SARS-COV-2 B.1.1.7 (Alpha) VARIANT / B.1.351 (Beta) VARIANT / P.1 (Gamma) VARIANT / B.1.617.2 (Delta) VARIANT / ANTIBODY / RECEPTOR-BINDING-DOMAIN / SPIKE / NEUTRALISATION / VIRAL PROTEIN/IMMUNE SYSTEM / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homologyD-MALATE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/ N00065X/1 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
CitationJournal: Cell Host Microbe / Year: 2022
Title: The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Authors: Chang Liu / Daming Zhou / Rungtiwa Nutalai / Helen M E Duyvesteyn / Aekkachai Tuekprakhon / Helen M Ginn / Wanwisa Dejnirattisai / Piyada Supasa / Alexander J Mentzer / Beibei Wang / James ...Authors: Chang Liu / Daming Zhou / Rungtiwa Nutalai / Helen M E Duyvesteyn / Aekkachai Tuekprakhon / Helen M Ginn / Wanwisa Dejnirattisai / Piyada Supasa / Alexander J Mentzer / Beibei Wang / James Brett Case / Yuguang Zhao / Donal T Skelly / Rita E Chen / Sile Ann Johnson / Thomas G Ritter / Chris Mason / Tariq Malik / Nigel Temperton / Neil G Paterson / Mark A Williams / David R Hall / Daniel K Clare / Andrew Howe / Philip J R Goulder / Elizabeth E Fry / Michael S Diamond / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape ...Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape from natural or vaccine-induced immunity. Beta is particularly difficult to neutralize using serum induced by early pandemic SARS-CoV-2 strains and is most antigenically separated from Delta. To understand this, we generated 674 mAbs from Beta-infected individuals and performed a detailed structure-function analysis of the 27 most potent mAbs: one binding the spike N-terminal domain (NTD), the rest the receptor-binding domain (RBD). Two of these RBD-binding mAbs recognize a neutralizing epitope conserved between SARS-CoV-1 and -2, while 18 target mutated residues in Beta: K417N, E484K, and N501Y. There is a major response to N501Y, including a public IgVH4-39 sequence, with E484K and K417N also targeted. Recognition of these key residues underscores why serum from Beta cases poorly neutralizes early pandemic and Delta viruses.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Beta-32 heavy chain
L: Beta-32 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6059
Polymers48,0462
Non-polymers5597
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-54 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.583, 66.848, 135.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Beta-32 heavy chain


Mass: 24742.602 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 Beta-32 light chain


Mass: 23303.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 396 molecules

#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.1 M DL-Malic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→68 Å / Num. obs: 61012 / % possible obs: 99.9 % / Redundancy: 43.4 % / Biso Wilson estimate: 32.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.027 / Net I/σ(I): 13.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 17.7 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2917 / CC1/2: 0.705 / % possible all: 96.4

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Processing

Software
NameVersionClassification
GDA1.19_4092data collection
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BEH

7beh


Resolution: 1.7→47.5 Å / SU ML: 0.2485 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.4041
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1884 3002 4.97 %
Rwork0.1678 57392 -
obs0.1688 60394 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 33 389 3770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583507
X-RAY DIFFRACTIONf_angle_d0.83064782
X-RAY DIFFRACTIONf_chiral_restr0.0566528
X-RAY DIFFRACTIONf_plane_restr0.0067612
X-RAY DIFFRACTIONf_dihedral_angle_d13.21721260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.42721130.44792299X-RAY DIFFRACTION83.52
1.73-1.760.45331080.40482592X-RAY DIFFRACTION94.87
1.76-1.790.38491320.33772710X-RAY DIFFRACTION98.65
1.79-1.820.30721320.28392711X-RAY DIFFRACTION99.54
1.82-1.860.27491480.21872735X-RAY DIFFRACTION100
1.86-1.90.22371570.18612727X-RAY DIFFRACTION100
1.9-1.950.21271500.17382691X-RAY DIFFRACTION100
1.95-20.19481370.17992745X-RAY DIFFRACTION100
2-2.050.19881450.18562741X-RAY DIFFRACTION100
2.05-2.110.22211500.18942745X-RAY DIFFRACTION100
2.11-2.180.21891470.1772720X-RAY DIFFRACTION100
2.18-2.260.19761530.17012755X-RAY DIFFRACTION100
2.26-2.350.21321510.16892746X-RAY DIFFRACTION100
2.35-2.450.18671380.1752754X-RAY DIFFRACTION100
2.45-2.580.21081590.17842751X-RAY DIFFRACTION100
2.58-2.740.1971580.18082754X-RAY DIFFRACTION100
2.74-2.960.18111560.1732758X-RAY DIFFRACTION100
2.96-3.250.17371430.16472792X-RAY DIFFRACTION100
3.25-3.720.17281440.14652823X-RAY DIFFRACTION100
3.72-4.690.14531490.12692841X-RAY DIFFRACTION100
4.69-47.50.17261320.15833002X-RAY DIFFRACTION99.87
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)
12.325689421760.2307658030351.390935163612.078135690921.029464435062.997598127410.0206514292383-0.029800438643-0.1383654006030.1938561622620.0650608212931-0.2564559842270.2207608007680.190451923511-0.07332482378650.2949404283510.0369750896416-0.04311444608770.201215605829-0.02665378592330.295588307593-18.450131382-7.03244901406-20.0599130513
21.25342593277-0.153945261269-0.9712861736121.860115899991.142990162191.31593210533-0.116286043468-0.0135206815352-0.000216405589881-0.1008177791010.073156872973-0.0105213126944-0.1908815316620.02828898706450.02129740736410.2631401531570.00727301627558-0.01307764864520.180272800423-0.0151011204850.26873077067-21.6081054073-0.203936324244-21.414167358
31.571972103080.001760882649521.863291705480.50370339274-1.365803867815.92277090096-0.411604991597-1.166925856791.008855664190.4875528899620.670886300245-0.592857938862-0.658430624415-0.28082584263-0.1889202069110.3805543926030.02421692078050.0501619048280.589896525002-0.1574784423340.441636804831-30.993587584818.670827231610.751491571
43.2114828468-2.02282729615-0.8474440981481.712308313880.4871366842351.35954744526-0.0633175146916-0.150337793004-0.1597767804840.1799158513680.03946237757960.1161686663090.1460730986220.0467504287474-0.016247517180.2429157565610.00128585640345-0.01792169347660.333672966814-0.03593737178880.272848433933-27.780194592210.66367426382.24360219776
52.80047033144-2.85406618985-3.687023953493.266486236333.906994538566.27075153497-0.0796287562751-0.832994540797-0.3639236652170.7228419220550.1465606316010.006002294209140.170953120155-0.204232093680.03315367049170.515872215317-0.04891032706250.1054174388010.506859070076-0.006035100716650.466692503596-32.63723396596.354924504319.47075539842
62.4382219485-0.9765299344380.5916771386423.878004821240.6487034028742.01124664603-0.0373209478555-0.01951889107690.271949554977-0.1879969890660.0347528207463-0.618866777141-0.2619704050730.5081441117190.08421267677850.301894279525-0.0517670457215-0.005556862918970.3034547107630.08488499725130.381344488145-16.665523747519.9461958298-28.9109696536
72.51003953242-0.7064940858961.113786023843.12294750694-0.03105939682982.07271850287-0.003691339545810.3383333745590.172534527288-0.237330003511-0.068447784222-0.06519865357040.06636935652190.1130312394740.0726932956660.292109614130.001937560717740.01302426095550.2350773169570.02349500137050.243684003935-24.282078082512.8228273502-31.6850585526
82.87555945207-1.336574448710.02865630927793.760224975281.294326169392.231562348620.06264825507380.268155889430.269361737467-0.07049586194330.00472952332195-0.3678789803910.0630286753891-0.06299367409640.0612852689560.255683681824-0.01848293433610.003621804163730.232569191240.01168317746260.240364549325-20.395280371812.3101544314-27.0048212718
92.34870045435-1.95155585299-1.553069652453.861646534082.17842311433.823102956480.0574424793415-0.1406298149610.389222560613-0.2698432109310.274382837516-0.176066053735-0.4586250253260.273654516306-0.4941880015010.322714748592-0.00874773996508-0.01562039875570.254310777455-0.03184300023840.310278135148-23.332792397328.1288838215-13.5592071099
103.31309493075-0.9314494074140.679409610493.98508789239-1.187429049484.61157651401-0.018885282273-0.747432531874-0.1764432805240.5047775183270.216489400490.2358256605310.373169097927-0.328610300486-0.185464628980.375109926577-0.00126472752516-0.01198111687060.552273053257-0.05232477028780.267156820861-25.10484450715.62898253814.5591973002
112.11818331249-0.6899026775441.017869685471.98087046303-1.459451274484.79274952114-0.0174876345717-0.2924505123010.2749034981080.02252370480060.126519342496-0.0450573889027-0.1832191560720.173964639686-0.01226032443280.267297583025-0.009961404802940.002730159948750.393026331189-0.1302898669430.323567343155-19.869267805625.6775876273.64317053651
121.23665260965-0.7955045784690.2941233200541.64599449234-0.2835731386743.668233109880.074992715518-0.591561206260.1949571353130.1908359495340.0762126282329-0.0320263501218-0.0704679021223-0.106082762716-0.06110643904060.233266613487-0.0140838063589-0.004145221043230.345489141409-0.09983006127850.270428434211-19.77059835323.38324917590.837515229978
132.19911289959-0.5605771300090.6405740917682.32484877597-0.6528037515883.22858724686-0.0924233987511-0.7112451334110.262930742520.760256045330.128458207120.0366569091264-0.5421809629650.155515301306-0.0654566622610.4294619292350.0272391851576-0.008364053007420.527860223049-0.1810558095980.321900872551-20.27424706525.565145286413.9359950588
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 91 )HA1 - 911 - 91
22chain 'H' and (resid 92 through 131 )HA92 - 13192 - 131
33chain 'H' and (resid 132 through 146 )HA132 - 146132 - 146
44chain 'H' and (resid 147 through 215 )HA147 - 215147 - 215
55chain 'H' and (resid 216 through 227 )HA216 - 227216 - 227
66chain 'L' and (resid 1 through 25 )LF1 - 251 - 25
77chain 'L' and (resid 26 through 75 )LF26 - 7526 - 75
88chain 'L' and (resid 76 through 101 )LF76 - 10176 - 101
99chain 'L' and (resid 102 through 113 )LF102 - 113102 - 113
1010chain 'L' and (resid 114 through 128 )LF114 - 128114 - 128
1111chain 'L' and (resid 129 through 150 )LF129 - 150129 - 150
1212chain 'L' and (resid 151 through 174 )LF151 - 174151 - 174
1313chain 'L' and (resid 175 through 213 )LF175 - 213175 - 213

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