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- PDB-9au1: SARS-CoV-2 XBB.1.5 RBD bound to the VIR-7229 and the S309 Fab fra... -

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Basic information

Entry
Database: PDB / ID: 9au1
TitleSARS-CoV-2 XBB.1.5 RBD bound to the VIR-7229 and the S309 Fab fragments
Components
  • (VIR-7229 Fab ...) x 2
  • S309 Fab heavy chain
  • S309 Fab light chain
  • SARS-CoV-2 XBB.1.5 RBD
KeywordsVIRAL PROTEIN / Sarbecoviruses / Spike glycoprotein / fusion protein / neutralizing antibodies / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homologyACETIC ACID / :
Function and homology information
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsRietz, T. / Park, Y.J. / Errico, J. / Czudnochowski, N. / Nix, J.C. / Corti, D. / Snell, G. / Marco, A.D. / Pinto, D. / Cameroni, E. ...Rietz, T. / Park, Y.J. / Errico, J. / Czudnochowski, N. / Nix, J.C. / Corti, D. / Snell, G. / Marco, A.D. / Pinto, D. / Cameroni, E. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler, D. / Structural Genomics Consortium (SGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: Cell / Year: 2024
Title: A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Authors: Laura E Rosen / M Alejandra Tortorici / Anna De Marco / Dora Pinto / William B Foreman / Ashley L Taylor / Young-Jun Park / Dana Bohan / Tyson Rietz / John M Errico / Kevin Hauser / Ha V ...Authors: Laura E Rosen / M Alejandra Tortorici / Anna De Marco / Dora Pinto / William B Foreman / Ashley L Taylor / Young-Jun Park / Dana Bohan / Tyson Rietz / John M Errico / Kevin Hauser / Ha V Dang / Justin W Chartron / Martina Giurdanella / Giuseppe Cusumano / Christian Saliba / Fabrizia Zatta / Kaitlin R Sprouse / Amin Addetia / Samantha K Zepeda / Jack Brown / Jimin Lee / Exequiel Dellota / Anushka Rajesh / Julia Noack / Qiqing Tao / Yvonne DaCosta / Brian Tsu / Rima Acosta / Sambhavi Subramanian / Guilherme Dias de Melo / Lauriane Kergoat / Ivy Zhang / Zhuoming Liu / Barbara Guarino / Michael A Schmid / Gretja Schnell / Jessica L Miller / Florian A Lempp / Nadine Czudnochowski / Elisabetta Cameroni / Sean P J Whelan / Hervé Bourhy / Lisa A Purcell / Fabio Benigni / Julia di Iulio / Matteo Samuele Pizzuto / Antonio Lanzavecchia / Amalio Telenti / Gyorgy Snell / Davide Corti / David Veesler / Tyler N Starr /
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has resulted in viral escape from clinically authorized monoclonal antibodies (mAbs), creating a need for mAbs that are ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has resulted in viral escape from clinically authorized monoclonal antibodies (mAbs), creating a need for mAbs that are resilient to epitope diversification. Broadly neutralizing coronavirus mAbs that are sufficiently potent for clinical development and retain activity despite viral evolution remain elusive. We identified a human mAb, designated VIR-7229, which targets the viral receptor-binding motif (RBM) with unprecedented cross-reactivity to all sarbecovirus clades, including non-ACE2-utilizing bat sarbecoviruses, while potently neutralizing SARS-CoV-2 variants since 2019, including the recent EG.5, BA.2.86, and JN.1. VIR-7229 tolerates extraordinary epitope variability, partly attributed to its high binding affinity, receptor molecular mimicry, and interactions with RBM backbone atoms. Consequently, VIR-7229 features a high barrier for selection of escape mutants, which are rare and associated with reduced viral fitness, underscoring its potential to be resilient to future viral evolution. VIR-7229 is a strong candidate to become a next-generation medicine.
History
DepositionFeb 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: 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
M: S309 Fab heavy chain
N: S309 Fab light chain
H: VIR-7229 Fab heavy chain
L: VIR-7229 Fab light chain
R: SARS-CoV-2 XBB.1.5 RBD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,03811
Polymers123,3565
Non-polymers6836
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-53 kcal/mol
Surface area45750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.726, 112.525, 170.314
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 , 4 types, 4 molecules MNHL

#1: Antibody S309 Fab heavy chain


Mass: 24573.471 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 S309 Fab light chain


Mass: 22971.406 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: Antibody VIR-7229 Fab heavy chain


Mass: 24368.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody VIR-7229 Fab light chain


Mass: 22993.303 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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Protein / Sugars , 2 types, 2 molecules R

#10: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Protein SARS-CoV-2 XBB.1.5 RBD


Mass: 28449.012 Da / Num. of mol.: 1 / Fragment: RBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Strain: XBB.1.5 / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 75 molecules

#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#9: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M carboxylic acids (0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate tribasic dihydrate, 0.02 M potassium sodium tartrate tetrahydrate, 0.02 M sodium oxamate), 0.1 M ...Details: 0.1 M carboxylic acids (0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate tribasic dihydrate, 0.02 M potassium sodium tartrate tetrahydrate, 0.02 M sodium oxamate), 0.1 M buffer system 2 pH 7.5 (sodium HEPES, MOPS) and 30% precipitant mix 2 (20% v/v ethylene glycol, 10% w/v PEG 8000)

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.195 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.195 Å / Relative weight: 1
ReflectionResolution: 2.41→44.98 Å / Num. obs: 55433 / % possible obs: 99.88 % / Redundancy: 13.2 % / Biso Wilson estimate: 60.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.164 / Net I/σ(I): 13.3
Reflection shellResolution: 2.41→2.45 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2722 / CC1/2: 0.318

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHASER2.8.3phasing
XDSJune 30, 2023data reduction
Aimless0.7.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→44.98 Å / SU ML: 0.4952 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.1305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2574 2757 4.97 %
Rwork0.2266 52676 -
obs0.2282 55433 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.42 Å2
Refinement stepCycle: LAST / Resolution: 2.41→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8075 0 42 70 8187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00758321
X-RAY DIFFRACTIONf_angle_d0.94111340
X-RAY DIFFRACTIONf_chiral_restr0.05271265
X-RAY DIFFRACTIONf_plane_restr0.00571451
X-RAY DIFFRACTIONf_dihedral_angle_d15.83252941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.450.43691230.42552599X-RAY DIFFRACTION99.82
2.45-2.50.46161170.4112600X-RAY DIFFRACTION99.96
2.5-2.540.43261350.40632627X-RAY DIFFRACTION99.89
2.54-2.60.41181530.39832531X-RAY DIFFRACTION99.78
2.6-2.650.41321370.40012645X-RAY DIFFRACTION99.71
2.65-2.710.43651520.39482544X-RAY DIFFRACTION99.81
2.71-2.780.39131420.36932602X-RAY DIFFRACTION100
2.78-2.860.33751310.3492644X-RAY DIFFRACTION99.89
2.86-2.940.32591190.30662630X-RAY DIFFRACTION99.78
2.94-3.040.34841400.31332610X-RAY DIFFRACTION99.85
3.04-3.140.34491420.29632607X-RAY DIFFRACTION99.93
3.14-3.270.36491400.30362612X-RAY DIFFRACTION99.96
3.27-3.420.30341400.26992599X-RAY DIFFRACTION99.89
3.42-3.60.26391270.23112641X-RAY DIFFRACTION99.86
3.6-3.830.25861550.21312637X-RAY DIFFRACTION99.93
3.83-4.120.24441160.192673X-RAY DIFFRACTION99.93
4.12-4.530.18891390.15492665X-RAY DIFFRACTION100
4.53-5.190.1671260.14382693X-RAY DIFFRACTION99.96
5.19-6.530.20251470.17162707X-RAY DIFFRACTION100
6.54-44.980.19851760.18042810X-RAY DIFFRACTION99.8
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)
10.931181001152-0.6046113430930.06630315279074.180562714320.3661823541421.400443167870.140069578281-0.0671456415691-0.2501003305050.1361163292740.02534879154170.4737511663110.108269177976-0.28386518348-0.1487775519650.460855458138-0.01621521915580.05357766457980.5965193574850.050561763020.97891742234-36.2923581747-6.5207749241915.4027620024
24.19779983856-1.37726617746-1.302687098963.41750090741-1.604559219836.98982410655-0.1154407943570.1224697269590.307336474618-0.117184975425-0.06320396654270.0626960809298-0.1273498555820.3316651088360.1426897456260.3764836372720.0107314542686-0.02135643180450.49805741972-0.004778230369160.785020172054-28.367941990325.0080189961-3.11054832199
31.162559076852.07246747778-0.9393610398334.59988384234-2.648982681412.93948794384-0.0336152837787-0.0437582666346-0.26002428501-0.350505710172-0.20607175302-0.910040222920.3478593177650.3531915674580.2740360839010.5754819871910.1124653167710.05905949358370.5722683299970.1041711463130.982678427407-14.5698027959-7.377726262699.59275938357
43.446345176111.33069676353-0.7487119939494.91557863571.349316833943.07989882906-0.0051126304141-0.2843529777780.2726123322440.2528491796-0.1696408784440.0220683236689-0.05908736356740.07968654850680.1564361140930.4281974093350.0274142967089-0.01110127553640.5722385459670.01965708024320.860586793791-16.114179131628.19245334526.39882262431
54.42765426422-3.620648827930.2605504489044.50604499607-0.09047230410450.629295850733-0.266485200508-0.429680048667-0.2981165883270.2807950363330.3369755213010.0894945722037-0.0623994104377-0.0835276117082-0.08072543163220.6498939702450.0129697194548-0.04789387996820.5333217769390.0195577319430.81503612451-4.10404021508-63.70354111843.353734628
63.077019637150.899779970769-0.3102980225715.78778306381-0.3318621113196.20829733162-0.09099166105040.1247223220670.313823427683-0.0716731801426-0.096961224038-0.826475481097-0.03648872559380.7954174428120.1894165211560.487142414670.0206053431382-0.04154860923190.520041695730.03169528205840.81013177303831.01356887-79.117198924143.1950925577
74.66019511383-3.49710926578-0.06819181551432.540082871660.1880980270511.00692613219-0.006839083724370.09812873079770.376689575736-0.201201131275-0.076067905222-0.692919229442-0.1521917238460.1328990389060.06975142770320.678242703576-0.05441481324130.0194567393370.4583645347150.09769372170360.9449760829058.43396887937-51.647514082729.4780318124
83.5695264769-2.48448571946-0.9276457120176.168237412683.45164608345.082313043470.05243859563580.3251111961380.325598459734-0.219252826497-0.159847872181-0.543618777839-0.08380641735260.1125850479710.09976544522990.502849895277-0.0304948608615-0.003920685084840.5436166016730.1330055452580.84215176330526.636944166-75.319025414427.5267298102
95.4881805195-2.134619980232.237302672291.19680010181-1.718821333624.19565323880.2021032504830.5752734745770.0331839779341-0.350449574199-0.1291500736780.3306872590760.059190753086-0.112787776222-0.05549432591620.712114356404-0.0543605083066-0.1446342901670.5040839672450.00854318143520.837192049322-31.7252029025-35.863290733314.36918566
101.96459259842-0.8922461949540.8402149686722.10254708116-0.7184785127353.01491731986-0.0122268263678-0.02174295537640.0344260855782-0.0554152089580.06371655059040.1316720794690.19210282034-0.0645456265634-0.05616545118980.672812798391-0.0483921782752-0.06380924885360.4546389406560.00841204747360.879639163104-19.9847540985-39.367045938227.2695124715
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'M' and (resid 1 through 128 )MA1 - 1281 - 128
22chain 'M' and (resid 129 through 230 )MA129 - 230129 - 230
33chain 'N' and (resid 1 through 108 )NB1 - 1081 - 108
44chain 'N' and (resid 109 through 212 )NB109 - 212109 - 212
55chain 'H' and (resid 1 through 128 )HC1 - 1281 - 128
66chain 'H' and (resid 129 through 223 )HC129 - 223129 - 219
77chain 'L' and (resid 2 through 122 )LF2 - 1222 - 122
88chain 'L' and (resid 123 through 212 )LF123 - 212123 - 212
99chain 'R' and (resid 333 through 393 )RH333 - 3931 - 58
1010chain 'R' and (resid 394 through 528 )RH394 - 52859 - 195

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