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- PDB-9ecx: Crystal structure of the SARS-CoV-2 NTD-targeted neutralizing ant... -

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Basic information

Entry
Database: PDB / ID: 9ecx
TitleCrystal structure of the SARS-CoV-2 NTD-targeted neutralizing antibody WRAIR-2008
Components
  • WRAIR-2008 Fab heavy chain
  • WRAIR-2008 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / neutralizing antibody / human antibody / SARS-CoV-2
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsJensen, J.L. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-18-2-0040 United States
CitationJournal: mBio / Year: 2025
Title: First-generation N-terminal domain supersite public antibodies retain activity against Omicron-derived lineages and protect mice against Omicron BA.5 challenge.
Authors: Vincent Dussupt / Jaime L Jensen / Paul V Thomas / Letzibeth Mendez-Rivera / Kerri G Lal / Michelle Zemil McCrea / Isabella Swafford / Joana Hernandez / Rajeshwer S Sankhala / Mekhala Rao / ...Authors: Vincent Dussupt / Jaime L Jensen / Paul V Thomas / Letzibeth Mendez-Rivera / Kerri G Lal / Michelle Zemil McCrea / Isabella Swafford / Joana Hernandez / Rajeshwer S Sankhala / Mekhala Rao / Juhi Arora / Agnes Hajduczki / Ningbo Jian / Phyllis A Rees / Indica Showell-De Leon / Gabriel Smith / Lauren Smith / Diana Wasson / Annika Schmid / I-Ting Teng / Tongqing Zhou / Peter D Kwong / Jeffrey R Currier / William W Reiley / Dominic Paquin-Proulx / Victoria R Polonis / Natalie D Collins / Nelson L Michael / M Gordon Joyce / Shelly J Krebs /
Abstract: Monoclonal antibodies to SARS-CoV-2 can offer prophylactic and therapeutic protection against severe disease, with particular utility for immunosuppressed and vulnerable populations. With the ...Monoclonal antibodies to SARS-CoV-2 can offer prophylactic and therapeutic protection against severe disease, with particular utility for immunosuppressed and vulnerable populations. With the constant emergence of new variants, understanding the neutralizing potency of monoclonal antibodies to dynamic spike protein epitopes is crucial. We show that a set of VH1-24-derived N-terminal domain (NTD)-directed antibodies, isolated from a convalescent donor early in the pandemic, displayed remarkable neutralization resilience against many Omicron SARS-CoV-2 variants, including BA.2, BA.5, and BQ.1.1. Neutralization potency to these Omicron variants is associated with slower off-rates to the spike protein. Structural characterization of the most potent NTD antibody, WRAIR-2008, revealed a conserved mode of interaction shared with other antibodies of the same multi-donor class. WRAIR-2008 protected mice from weight loss following BA.5 challenge and reduced infectious viral titers in the lungs. Our study highlights the retention of neutralization activity and protection of first-generation VH1-24-derived NTD-directed antibodies to specific Omicron variants and provides valuable insights into the shifting landscape of SARS-CoV-2 variants that are vulnerable to select monoclonal antibodies.
IMPORTANCE: As SARS-CoV-2 circulating variants evolve, it is important to understand the vulnerabilities of these viruses to neutralizing antibodies. Within this manuscript, we describe first- ...IMPORTANCE: As SARS-CoV-2 circulating variants evolve, it is important to understand the vulnerabilities of these viruses to neutralizing antibodies. Within this manuscript, we describe first-generation antibodies isolated following infection with WA-1 that retain viral neutralization to subsequent Omicron variants by targeting a site of viral vulnerability called the NTD. This work highlights the shifting landscape of SARS-CoV-2 variants and provides mechanistic insights into how antibodies from prior infections may play a role in preventing subsequent SARS-CoV-2 variant infections.
History
DepositionNov 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 22, 2025Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: WRAIR-2008 Fab heavy chain
L: WRAIR-2008 Fab light chain
C: WRAIR-2008 Fab heavy chain
D: WRAIR-2008 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,13913
Polymers97,2994
Non-polymers8419
Water1,838102
1
H: WRAIR-2008 Fab heavy chain
L: WRAIR-2008 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2068
Polymers48,6492
Non-polymers5576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-51 kcal/mol
Surface area19620 Å2
MethodPISA
2
C: WRAIR-2008 Fab heavy chain
D: WRAIR-2008 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9345
Polymers48,6492
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-59 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.040, 60.400, 92.770
Angle α, β, γ (deg.)90.00, 99.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody WRAIR-2008 Fab heavy chain


Mass: 24542.334 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 WRAIR-2008 Fab light chain


Mass: 24106.947 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.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.17 M ammonium sulfate, 25.5% w/v PEG 4000, 15% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 2.647→34.175 Å / Num. obs: 27956 / % possible obs: 99.7 % / Redundancy: 3.9 % / CC1/2: 0.978 / Net I/σ(I): 4.4
Reflection shellResolution: 2.647→2.692 Å / Num. unique obs: 1333 / CC1/2: 0.331

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→34.17 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2888 1037 4.95 %
Rwork0.2226 --
obs0.2259 20933 76.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.67→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6812 0 51 102 6965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097008
X-RAY DIFFRACTIONf_angle_d1.439528
X-RAY DIFFRACTIONf_dihedral_angle_d18.4912516
X-RAY DIFFRACTIONf_chiral_restr0.0671077
X-RAY DIFFRACTIONf_plane_restr0.012108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.810.3727230.291404X-RAY DIFFRACTION11
2.81-2.980.3699640.27931416X-RAY DIFFRACTION38
2.98-3.210.34041630.26823153X-RAY DIFFRACTION85
3.21-3.540.33631900.22833721X-RAY DIFFRACTION100
3.54-4.050.27161940.21753692X-RAY DIFFRACTION99
4.05-5.10.25791990.18743709X-RAY DIFFRACTION99
5.1-34.170.27012040.22733801X-RAY DIFFRACTION99
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)
13.11840.2659-0.33522.6129-0.77442.51810.01510.075-0.110.2956-0.0506-0.3829-0.16430.66230.20190.3040.0671-0.12650.5202-0.08880.4366-10.7389-3.9342-29.3353
21.99982.9993-1.33058.249-5.93217.6068-0.37081.6468-1.6871-1.4037-0.3072-1.8432.36871.5622-1.15951.16870.16060.01011.3417-0.39351.2715-7.4444-18.423-40.002
30.79860.93810.16292.26881.09140.98450.0213-0.22120.0090.2085-0.19040.0769-0.0285-0.27030.02250.3254-0.0492-0.03570.12780.03620.2409-38.0218-11.5491-38.318
40.6304-0.10750.74780.4663-0.11030.88770.0744-0.13910.0290.09230.0416-0.01210.02630.00880.00080.82350.0602-0.18951.1730.27681.8876-56.2835-14.6781-44.3551
53.0237-1.47670.98363.34083.01014.9511-0.2096-0.32940.7493-1.02690.3384-0.6298-0.83970.7336-0.06260.9669-0.2693-0.07510.5705-0.03670.5508-10.75411.6544-55.3073
62.22960.09151.17452.67080.44431.43530.0108-0.05540.173-0.10620.0024-0.7443-0.57931.07540.15910.4508-0.13610.12460.8995-0.13090.6067-5.4982-5.6149-50.6199
70.47940.40780.2790.33960.23370.1591-0.0155-0.759-0.5850.31480.3515-0.28840.18670.4865-0.52140.65130.5135-0.21671.1343-0.14820.7694-3.4053-15.3253-51.7767
80.169-0.34120.38811.60560.6192.49950.0935-0.17030.186-0.2073-0.0056-0.5174-0.14730.9551-0.24450.4009-0.11190.06240.5476-0.12670.3004-11.3999-5.8388-53.9961
90.87230.1552-0.67380.7830.1792.59390.10240.0354-0.0074-0.23880.03610.1801-0.0677-0.1776-0.04390.27840.0066-0.01630.11390.00480.2568-44.6042-4.6424-48.7389
102.0250.5274-0.22832.6053-1.28242.6350.03990.5137-0.2944-0.30280.08930.8073-0.2608-0.7569-0.32340.4049-0.0038-0.0750.2868-0.03970.4586-52.0736-6.3048-54.5538
110.45350.15680.70470.11420.20620.93830.03790.3840.51390.44590.14740.9663-0.5477-1.21310.37270.44610.25460.15590.8160.25881.0155-73.279-8.82756.7005
120.6743-0.6550.2012.69380.190.12480.33452.13931.0324-0.46650.17951.9209-0.4819-1.2028-0.16850.74920.24610.27551.6380.50311.7105-72.08575.0671-5.0223
131.22610.21520.02260.28670.16850.65410.0781-0.6379-0.37620.2724-0.061-0.24790.53610.03810.46610.22030.23470.0195-0.2233-0.05590.1865-44.173-0.64387.6841
143.83132.8515-0.92152.1959-1.08612.04660.1487-0.5607-0.7583-0.8312-0.23870.10610.47250.0224-0.37310.43080.1810.03540.57810.00710.8314-63.8127-14.5336-17.1532
151.35620.7135-1.0321.3794-0.21720.99660.26740.0685-0.7947-0.21010.24550.6989-0.0321-0.6851-0.4750.6171-0.0554-0.20740.64560.30740.9758-74.2728-10.8472-19.3076
166.3166-0.4827-1.45462.551-0.63524.74110.3337-0.42130.65660.4290.29780.0012-0.20150.26351.57280.29720.03-0.04730.37590.17730.5758-65.9619-3.3025-9.709
170.36690.15650.07930.22560.03970.73310.0455-0.0938-0.1645-0.3938-0.00590.4986-0.2212-0.17020.46130.73350.3036-0.05570.60010.48210.7843-73.01661.9471-16.9173
181.4862-1.12230.45440.91510.04212.00610.18970.4209-0.2472-0.65080.36530.9461-0.0829-0.52530.94160.46710.036-0.1570.56980.27740.4559-66.0409-5.0703-18.467
191.1880.08570.03690.79430.36350.62080.1414-0.0196-0.41640.03280.25180.3038-0.3225-0.34530.16560.25430.0162-0.05820.27850.2220.3745-49.5561-6.7633-4.4386
200.4791-0.23280.20860.7061-0.34320.56860.1178-0.0519-0.2857-0.4408-0.1789-0.08450.10270.0229-0.04740.43680.02250.0708-0.02860.16670.0916-35.0254-7.8207-5.2609
210.894-0.43971.11950.7141-0.88752.0203-0.14390.28550.22320.2186-0.09-0.2853-0.03220.5401-0.13880.23460.0594-0.04480.1489-0.07860.5432-31.6937-8.1156-1.9152
227.5731-6.46467.71347.1751-7.04547.98470.0404-0.0693-0.00470.12210.04-0.09770.16040.2034-0.16270.4460.1874-0.36760.9676-0.42841.0597-22.66050.95428.3307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 95 )
2X-RAY DIFFRACTION2chain 'A' and (resid 96 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 214 )
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 216 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 14 )
6X-RAY DIFFRACTION6chain 'B' and (resid 15 through 48 )
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 61 )
8X-RAY DIFFRACTION8chain 'B' and (resid 62 through 113 )
9X-RAY DIFFRACTION9chain 'B' and (resid 114 through 188 )
10X-RAY DIFFRACTION10chain 'B' and (resid 189 through 214 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 95 )
12X-RAY DIFFRACTION12chain 'C' and (resid 96 through 106 )
13X-RAY DIFFRACTION13chain 'C' and (resid 107 through 214 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 14 )
15X-RAY DIFFRACTION15chain 'D' and (resid 15 through 32 )
16X-RAY DIFFRACTION16chain 'D' and (resid 33 through 48 )
17X-RAY DIFFRACTION17chain 'D' and (resid 49 through 61 )
18X-RAY DIFFRACTION18chain 'D' and (resid 62 through 90 )
19X-RAY DIFFRACTION19chain 'D' and (resid 91 through 128 )
20X-RAY DIFFRACTION20chain 'D' and (resid 129 through 150 )
21X-RAY DIFFRACTION21chain 'D' and (resid 151 through 211 )
22X-RAY DIFFRACTION22chain 'D' and (resid 212 through 213 )

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