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- PDB-9pw4: Structure of V30V4 in complex with SARS-CoV-2 spike -

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Basic information

Entry
Database: PDB / ID: 9pw4
TitleStructure of V30V4 in complex with SARS-CoV-2 spike
Components
  • SP1-77 FAB HEAVY CHAIN
  • SP1-77 FAB LIGHT CHAIN
  • Spike protein S1
  • V30V4 FAB HEAVY CHAIN
  • V30V4 FAB LIGHT CHAIN
KeywordsVIRAL PROTEIN / SARS-Cov-2 G614 antibody
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsWang, Y.J. / Kibria, G. / Wesemann, D. / Chen, B.
Funding support United States, 1items
OrganizationGrant numberCountry
Massachusetts Consortium on Pathogen Readiness (MassCPR) United States
CitationJournal: Cell Rep / Year: 2025
Title: Affinity maturation and light-chain-mediated paratope diversification anticipates viral evolution.
Authors: John Dingus / Duck-Kyun Yoo / Sachin Kumar / Yajuan Wang / Md Golam Kibria / Shahab Saghaei / Zahra Allahyari / Jessica W Chen / Natalie M Caputo / Jason Hwang / Bing Chen / Duane R Wesemann /
Abstract: A key goal of vaccinology is to train the immune system to combat current pathogens while preparing it for future variants. Here, we investigate how Wuhan strain severe acute respiratory syndrome ...A key goal of vaccinology is to train the immune system to combat current pathogens while preparing it for future variants. Here, we investigate how Wuhan strain severe acute respiratory syndrome coronavirus 2 mRNA vaccination generates "anticipatory breadth" in an antibody family exhibiting germline complementarity to the ACE2 binding site on the receptor-binding-domain (RBD). IGHV3-53/66 antibodies from infection-naive vaccinees frequently neutralize Omicron variants and contain hallmark breadth-enhancing mutations. While Omicron breakthrough infection does not alter IGHV3-53/66 mutation frequencies, it modifies Ig light-chain pairing frequencies, suggesting variant-driven selection for favorable pairings. Structural analyses of IGHV3-53/66-RBD complexes show that hallmark heavy-chain mutations refine interactions with conserved RBD residues, while alternative Ig light-chain pairings modify contacts at Omicron mutation sites. Together, these findings support a cooperative model of anticipatory breadth involving targeting of a functionally constrained epitope, affinity maturation to establish an affinity buffer, and alternative Ig light-chain pairings to diversify paratopes-providing a mechanistic framework for anticipating viral evolution.
History
DepositionAug 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jan 14, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
D: V30V4 FAB LIGHT CHAIN
F: SP1-77 FAB LIGHT CHAIN
C: V30V4 FAB HEAVY CHAIN
E: SP1-77 FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,4046
Polymers171,6715
Non-polymers7331
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Antibody , 4 types, 4 molecules DFCE

#2: Antibody V30V4 FAB LIGHT CHAIN


Mass: 23545.100 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 SP1-77 FAB LIGHT CHAIN


Mass: 23294.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SP1-77 Fab is from a humanized murine antibody. / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Antibody V30V4 FAB HEAVY CHAIN


Mass: 24051.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody SP1-77 FAB HEAVY CHAIN


Mass: 24236.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SP1-77 Fab is from a humanized murine antibody. / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 76543.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: derived from the D614G variant, including signal sequence
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Structure of V30V4 in complex with SARS-CoV-2 spikeCOMPLEX#1-#50MULTIPLE SOURCES
2SARS-CoV-2 spike S1COMPLEX#11RECOMBINANT
3V30V4 FabCOMPLEX#2, #41RECOMBINANT
4SP1-77 FabCOMPLEX#3, #51RECOMBINANT
Molecular weightValue: 0.170 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrainDetails
22Severe acute respiratory syndrome coronavirus 22697049G614
33Homo sapiens (human)9606
44Mus musculus (house mouse)10090SP1-77 Fab is from a humanized murine antibody.
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Homo sapiens (human)9606
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 56.68 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 244319 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 88.14 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00258353
ELECTRON MICROSCOPYf_angle_d0.493611369
ELECTRON MICROSCOPYf_chiral_restr0.04141280
ELECTRON MICROSCOPYf_plane_restr0.00341460
ELECTRON MICROSCOPYf_dihedral_angle_d3.93561175

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