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- PDB-7zf8: SARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab -

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Basic information

Entry
Database: PDB / ID: 7zf8
TitleSARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab
Components
  • COVOX-150 heavy chain
  • COVOX-150 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Omicron / BA.1 / BA.2 / RBD / antibody / Fab / COVOX-150 / VIRAL PROTEIN/IMMUNE SYSTEM
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsZhou, D. / Huo, J. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Cell / Year: 2022
Title: Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / ...Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / Donal Skelly / Thomas G Ritter / Ali Amini / Sagida Bibi / Sandra Adele / Sile Ann Johnson / Bede Constantinides / Hermione Webster / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / Derrick Crook / Andrew J Pollard / Teresa Lambe / Philip Goulder / / Neil G Paterson / Mark A Williams / David R Hall / Juthathip Mongkolsapaya / Elizabeth E Fry / Wanwisa Dejnirattisai / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA. ...Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
History
DepositionApr 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: 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_PubMed / _citation.title
Revision 1.2Jun 22, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: COVOX-150 heavy chain
L: COVOX-150 light chain
E: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)69,9013
Polymers69,9013
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-26 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.225, 84.933, 58.421
Angle α, β, γ (deg.)90.000, 101.021, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody COVOX-150 heavy chain


Mass: 23415.322 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 COVOX-150 light chain


Mass: 23456.035 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: Protein Spike protein S1 / SARS-CoV-2 Omicron BA.2 Spike protein


Mass: 23030.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

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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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 18% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.95→96 Å / Num. obs: 19778 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 52.6 Å2 / CC1/2: 0.939 / Rmerge(I) obs: 0.49 / Rpim(I) all: 0.198 / Net I/σ(I): 2.1
Reflection shellResolution: 2.95→3 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 932 / CC1/2: 0.303 / % possible all: 99.8

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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: 7BEI

7bei


Resolution: 2.95→57.34 Å / SU ML: 0.4859 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.5339
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 976 5.04 %
Rwork0.2201 18383 -
obs0.2221 19359 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.6 Å2
Refinement stepCycle: LAST / Resolution: 2.95→57.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 0 0 4794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024916
X-RAY DIFFRACTIONf_angle_d0.5336692
X-RAY DIFFRACTIONf_chiral_restr0.0423745
X-RAY DIFFRACTIONf_plane_restr0.0047860
X-RAY DIFFRACTIONf_dihedral_angle_d11.1511748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.110.38781010.3522289X-RAY DIFFRACTION85.57
3.11-3.30.31411540.31142623X-RAY DIFFRACTION99.71
3.3-3.550.3171590.25532670X-RAY DIFFRACTION99.96
3.56-3.910.24851310.23212680X-RAY DIFFRACTION99.93
3.91-4.480.25131470.18732694X-RAY DIFFRACTION100
4.48-5.640.19091340.16192677X-RAY DIFFRACTION99.96
5.64-57.340.23441500.19572750X-RAY DIFFRACTION100
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)
13.637137676520.194832460669-0.08128067734971.99375169154-1.234171246633.08882936148-0.266843398961-0.263579718007-0.8457740892270.5931573585750.3039989127380.327838640890.502891570109-0.950524610692-0.03416122031350.533024989390.05873640641340.1277334104650.3511694380470.1510390129080.39923563740341.3188043049-7.7444650808713.1138635114
22.72209156593-0.103406828661-1.195934440811.55155286610.5043324144552.40873681337-0.0969009493057-0.00686781746544-0.1597657125360.1284121130150.0760552334294-0.0259402821901-0.0478051956442-0.2322008046550.04937960743870.3561986452250.06642347235420.01596029320770.3354609252390.01078091047590.22844968427646.7723823217-4.240637905787.27232048646
34.059802005161.013073464232.022487959681.548264184191.271538205265.824226364530.159383426533-0.6402038282390.2090097654120.125259868753-0.1952241561060.370392602989-0.173908631766-0.684941394024-0.1006324212940.3245705218630.08025022623110.1196409892730.5177416108810.1275624879480.4443751184710.05152138149.19218178115.5125895651
46.31213896517-0.3005920874982.097594549332.493496722950.2865261485532.768916453110.4996542580960.100487106116-0.7712542396640.3394360927730.2072012494570.6827204475920.4860798416560.0316153656669-0.5777942018220.372685221146-0.04604738291490.03079052286060.4098147273880.1427419261780.54255701421413.49891200491.9418576832714.1864711179
56.210656994370.8458983891690.5257887314870.7794529988961.356442694993.91146273210.287134504277-0.740284307341-0.4209995460510.3188598974610.4346773349621.04772806734-0.352535793762-0.457915841611-0.4855875634710.549506308015-0.06229418551650.2189548193990.6544319871560.2177631666550.5017845612396.638668099694.8330110776421.9760775508
68.268139356390.960934401334-0.855974264864.51770887511-0.7313471218732.716790549770.4947473649650.8044703634520.3803549374390.1365064979490.1728133484030.287525280051-0.770220311498-0.498879516973-0.198788593820.403009266122-0.00282229603540.03359582182820.361223171437-0.03872477048080.41360697332333.31711768646.47307479843-12.9522544004
74.17663423875-0.665118987279-0.8413631447873.97721892314-1.03914689182.90636159189-0.08222451932160.588216024742-0.403647634375-0.223770560099-0.120735206927-0.141505616666-0.0002374651776480.04611210813550.1154090376040.3689560674370.0845853582754-0.0214858353940.626242958226-0.03187821092340.14873554008540.1874377254-2.15478354501-12.4654280174
86.556523891190.905765481781-1.644963800123.66245578801-0.9023832704532.365394428580.03748606566960.748853097888-0.452030591266-0.2594308696250.0197747058112-0.0684428687757-0.295920841441-0.08196570832290.001304732429520.4368796636470.0919103810851-0.0003372916565540.618094160433-0.03537599376650.31473996321634.9469119541-0.50283631247-15.2329588823
92.071047004532.28955104515-3.101092613066.79387940231-0.8400237247156.27202134355-0.433158289779-1.342146884480.1532245929720.4323731848910.544244049888-1.46883669137-0.6221218272781.112424903470.122752709770.65440790332-0.09073590000880.0818867957480.642744559595-0.1311950676040.56312176694148.087038974.53486176913-5.93868506267
102.14374273957-0.83679695636-0.5081948037842.769603403091.248581758632.04545707742-0.2565051488480.0451646374298-0.08781018910390.09913850159620.312525118660.03186109395190.07484099403080.367003581526-0.04813959414470.2352498527650.015132355435-0.04785988286990.4570133281020.1212745195580.34988560181215.634442301913.14090564564.24286853945
112.20599526594-0.750986110048-0.3812321700663.160925048251.596665492423.61835729585-0.0753008897398-0.143505746437-0.1274912771380.1795211012650.1341530180180.143007520298-0.320136072562-0.388872647171-0.04684123512760.2635574932710.02238361062690.04874252660020.552704208270.09279650302380.45904151497812.152493475122.67314888759.53111544269
127.782002546691.114323621570.375285954222.320567990790.9883058463945.19638194607-0.09291999105640.8210889518380.229585255669-0.901546538749-0.391570991426-1.45686137844-0.5453037384310.7205417844830.1476991569150.479132017828-0.008464683501810.03305856846550.5181150011350.1244539559510.74129880323280.4710111208-0.388724123944-20.3343878904
132.59336407223-0.711474697503-2.87391916660.3083152561951.197542075655.501037220510.31058043488-0.3905866562410.488533301643-0.664239908746-0.141365583135-0.881318656766-1.698869334030.319395116309-0.2354655869240.878399540949-0.1056582930730.1164223819960.582732180299-0.06016674559381.2411723670483.25818335897.06352082657-13.8914696548
142.74918800623-1.24468906307-0.5517449871090.5646985930390.2375198397633.644258191460.308091878099-0.2343730280430.404479605894-0.671469946349-0.191297376209-1.34916643582-1.490586477821.19476469203-0.06367882372190.836234667718-0.707200317926-0.04284065255761.19546235608-0.1765769736522.0287036654490.8387169848.77872014101-5.66233516181
154.731326932080.4541711371120.04254438908222.477495419680.04496608370512.65138092422-0.0140895114920.172042601641-0.0684501894106-0.11314298286-0.104935492109-0.119496236465-0.00518114013661-0.07171148903910.1628310988360.306553079490.07246066003180.02066376667910.411278118457-0.04434325696090.26096440226865.3868306126-4.96450870985-11.7808434233
163.043554360831.528554250051.016957310216.882879631430.08223296602156.99698533380.1307998865720.163659704206-0.1595893543750.344532826936-0.088209993729-0.69885250786-0.2310872175070.8484812972390.07536839693450.672622612806-0.09261455181610.0517878322460.1404490810350.08186149146330.4013215031377.36833494843.00516357926-12.6842624419
172.16488192702-0.7282399898160.3654049274195.260264338215.427360974786.212446793920.231240800006-0.481626672074-0.9905005692611.60327732542-0.165995717811-2.25010736964-0.1080520686122.15894223087-0.1387279326271.47649342851-0.5397856982060.06668974009551.051442466530.3341739992651.5737946636295.570981478-0.865336095887-6.02412602937
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 17 )HA1 - 171 - 17
22chain 'H' and (resid 18 through 123 )HA18 - 12318 - 123
33chain 'H' and (resid 124 through 149 )HA124 - 149124 - 145
44chain 'H' and (resid 150 through 207 )HA150 - 207146 - 203
55chain 'H' and (resid 208 through 220 )HA208 - 220204 - 216
66chain 'L' and (resid 1 through 18 )LB1 - 181 - 18
77chain 'L' and (resid 19 through 61 )LB19 - 6119 - 61
88chain 'L' and (resid 62 through 89 )LB62 - 8962 - 89
99chain 'L' and (resid 90 through 104 )LB90 - 10490 - 104
1010chain 'L' and (resid 105 through 176 )LB105 - 176105 - 176
1111chain 'L' and (resid 177 through 215 )LB177 - 215177 - 215
1212chain 'E' and (resid 333 through 353 )EC333 - 3531 - 21
1313chain 'E' and (resid 354 through 380 )EC354 - 38022 - 48
1414chain 'E' and (resid 381 through 393 )EC381 - 39349 - 61
1515chain 'E' and (resid 394 through 506 )EC394 - 50662 - 174
1616chain 'E' and (resid 507 through 516 )EC507 - 516175 - 184
1717chain 'E' and (resid 517 through 527 )EC517 - 527185 - 195

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