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- EMDB-71899: Structure of V30V4 in complex with SARS-CoV-2 spike -

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Entry
Database: EMDB / ID: EMD-71899
TitleStructure of V30V4 in complex with SARS-CoV-2 spike
Map dataThe main map of Structure of V30V4 in complex with SARS-CoV-2 spike
Sample
  • Complex: Structure of V30V4 in complex with SARS-CoV-2 spike
    • Complex: SARS-CoV-2 spike S1
      • Protein or peptide: Spike protein S1
    • Complex: V30V4 Fab
      • Protein or peptide: V30V4 FAB LIGHT CHAIN
      • Protein or peptide: V30V4 FAB HEAVY CHAIN
    • Complex: SP1-77 Fab
      • Protein or peptide: SP1-77 FAB LIGHT CHAIN
      • Protein or peptide: SP1-77 FAB HEAVY CHAIN
KeywordsSARS-Cov-2 G614 antibody / VIRAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsWang YJ / Kibria G / Wesemann D / Chen B
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71899.png

Downloads & links

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Map

FileDownload / File: emd_71899.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe main map of Structure of V30V4 in complex with SARS-CoV-2 spike
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-2.1996255 - 2.935985
Average (Standard dev.)0.00019270724 (±0.045872223)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71899_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The raw map of Structure of V30V4 in complex with SARS-CoV-2 spike

Fileemd_71899_additional_1.map
AnnotationThe raw map of Structure of V30V4 in complex with SARS-CoV-2 spike
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_71899_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_71899_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of V30V4 in complex with SARS-CoV-2 spike

EntireName: Structure of V30V4 in complex with SARS-CoV-2 spike
Components
  • Complex: Structure of V30V4 in complex with SARS-CoV-2 spike
    • Complex: SARS-CoV-2 spike S1
      • Protein or peptide: Spike protein S1
    • Complex: V30V4 Fab
      • Protein or peptide: V30V4 FAB LIGHT CHAIN
      • Protein or peptide: V30V4 FAB HEAVY CHAIN
    • Complex: SP1-77 Fab
      • Protein or peptide: SP1-77 FAB LIGHT CHAIN
      • Protein or peptide: SP1-77 FAB HEAVY CHAIN

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Supramolecule #1: Structure of V30V4 in complex with SARS-CoV-2 spike

SupramoleculeName: Structure of V30V4 in complex with SARS-CoV-2 spike / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 170 KDa

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Supramolecule #2: SARS-CoV-2 spike S1

SupramoleculeName: SARS-CoV-2 spike S1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: G614

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Supramolecule #3: V30V4 Fab

SupramoleculeName: V30V4 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2, #4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: SP1-77 Fab

SupramoleculeName: SP1-77 Fab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3, #5
Source (natural)Organism: Mus musculus (house mouse) / Details: SP1-77 Fab is from a humanized murine antibody.

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1
Details: derived from the D614G variant, including signal sequence
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 76.543086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSF VIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ GVNCTEVPVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSPR RA

UniProtKB: Spike glycoprotein

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Macromolecule #2: V30V4 FAB LIGHT CHAIN

MacromoleculeName: V30V4 FAB LIGHT CHAIN / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.5451 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRVSQSVS SNSLAWYQQK PGQPPRLLIY GASSRATGIP DRFSGSGSGT DFTLTINRLE PEDFAVYYC QQYGSSPPIT FGQGTRLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
EIVLTQSPGT LSLSPGERAT LSCRVSQSVS SNSLAWYQQK PGQPPRLLIY GASSRATGIP DRFSGSGSGT DFTLTINRLE PEDFAVYYC QQYGSSPPIT FGQGTRLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #3: SP1-77 FAB LIGHT CHAIN

MacromoleculeName: SP1-77 FAB LIGHT CHAIN / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.294617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCQASQDIS DYLNWYQQQP GKAPKLLIYD ASNLETGVPS RFSGSGSGTD FTFTISSLQP EDIGTYYCQ QYDNLPTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
DIQMTQSPSS LSASVGDRVT ITCQASQDIS DYLNWYQQQP GKAPKLLIYD ASNLETGVPS RFSGSGSGTD FTFTISSLQP EDIGTYYCQ QYDNLPTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #4: V30V4 FAB HEAVY CHAIN

MacromoleculeName: V30V4 FAB HEAVY CHAIN / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.051916 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LIQPGGSLRL SCTASEIIVS RNYMSWVRQA PGKGLEWVSL IYAGGSTFYA DSVKGRFTIS RDDSKNTLYL QMNSLRAED TAVYYCARDL FEAGATDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
EVQLVESGGG LIQPGGSLRL SCTASEIIVS RNYMSWVRQA PGKGLEWVSL IYAGGSTFYA DSVKGRFTIS RDDSKNTLYL QMNSLRAED TAVYYCARDL FEAGATDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSCDKTHT

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Macromolecule #5: SP1-77 FAB HEAVY CHAIN

MacromoleculeName: SP1-77 FAB HEAVY CHAIN / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.236168 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYTFT GTYIHWVRQA PGQGLEWMGW INPNSGGTNF AQIFQGRVTL TRDTSISTAY MDLNRLKSD DTAVYYCARD RVLYGRSFGW YFDVWGAGTT VTVSSASTKG PSVFPLAPCS RSTSESTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYTFT GTYIHWVRQA PGQGLEWMGW INPNSGGTNF AQIFQGRVTL TRDTSISTAY MDLNRLKSD DTAVYYCARD RVLYGRSFGW YFDVWGAGTT VTVSSASTKG PSVFPLAPCS RSTSESTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTKTYTCN VDHKPSNTKV DKRVESK

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 56.68 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 244319
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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