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- EMDB-60101: SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, head-to-h... -

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Basic information

Entry
Database: EMDB / ID: EMD-60101
TitleSARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, head-to-head aggregate
Map data
Sample
  • Complex: SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, head-to-head aggregate
    • Complex: SARS-CoV-2 spike trimer (6P)
      • Protein or peptide: Spike glycoprotein,Fibritin,Expression Tag
    • Complex: R1-26 Fab
      • Protein or peptide: Heavy chain of R1-26 Fab
      • Protein or peptide: Light chain of R1-26 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSpike protein / RBD / Antibody / Fab / Viral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / viral translation / host extracellular space / 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 / viral translation / host extracellular space / 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
Fibritin C-terminal / Fibritin C-terminal region / 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. ...Fibritin C-terminal / Fibritin C-terminal region / 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
Fibritin / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.26 Å
AuthorsYan Q / Gao X / Liu B / Hou R / He P / Li Z / Chen Q / Wang J / He J / Chen L ...Yan Q / Gao X / Liu B / Hou R / He P / Li Z / Chen Q / Wang J / He J / Chen L / Zhao J / Xiong X
Funding support China, 3 items
OrganizationGrant numberCountry
Other government2021A1515011289 China
Other governmentSRPG22-002 China
Other governmentEKPG21-06 China
CitationJournal: Nat Commun / Year: 2024
Title: Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants.
Authors: Qihong Yan / Xijie Gao / Banghui Liu / Ruitian Hou / Ping He / Yong Ma / Yudi Zhang / Yanjun Zhang / Zimu Li / Qiuluan Chen / Jingjing Wang / Xiaohan Huang / Huan Liang / Huiran Zheng / ...Authors: Qihong Yan / Xijie Gao / Banghui Liu / Ruitian Hou / Ping He / Yong Ma / Yudi Zhang / Yanjun Zhang / Zimu Li / Qiuluan Chen / Jingjing Wang / Xiaohan Huang / Huan Liang / Huiran Zheng / Yichen Yao / Xianying Chen / Xuefeng Niu / Jun He / Ling Chen / Jincun Zhao / Xiaoli Xiong /
Abstract: Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants ...Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralizing public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron-specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes a potential immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidence to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.
History
DepositionMay 10, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60101.png

Downloads & links

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Map

FileDownload / File: emd_60101.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.75 Å/pix.
x 300 pix.
= 525.6 Å		1.75 Å/pix.
x 300 pix.
= 525.6 Å		1.75 Å/pix.
x 300 pix.
= 525.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.177
Minimum - Maximum-0.30937567 - 1.0538212
Average (Standard dev.)-0.00008910838 (±0.036274772)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 525.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60101_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60101_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, head-to-h...

EntireName: SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, head-to-head aggregate
Components
  • Complex: SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, head-to-head aggregate
    • Complex: SARS-CoV-2 spike trimer (6P)
      • Protein or peptide: Spike glycoprotein,Fibritin,Expression Tag
    • Complex: R1-26 Fab
      • Protein or peptide: Heavy chain of R1-26 Fab
      • Protein or peptide: Light chain of R1-26 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, head-to-h...

SupramoleculeName: SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, head-to-head aggregate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: SARS-CoV-2 spike trimer (6P)

SupramoleculeName: SARS-CoV-2 spike trimer (6P) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: R1-26 Fab

SupramoleculeName: R1-26 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike glycoprotein,Fibritin,Expression Tag

MacromoleculeName: Spike glycoprotein,Fibritin,Expression Tag / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 141.253875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV YSSANNCTFE Y VSQPFLMD ...String:
VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV YSSANNCTFE Y VSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QTLLALHRSY LT PGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRVQPTESIV RFP NITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSFVIRGDE VRQI APGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPCNGVEG FNCYF PLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFLPFQQ FGRDIA DTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGSNVF QTRAGCL IG AEHVNNSYEC DIPIGAGICA SYQTQTNSPG SASSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTISV TTEILPVS M TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGFN FSQILPDPS KPSKRSPIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GPALQIPFP MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STPSALGKLQ DVVNQNAQAL NTLVKQLSSN F GAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RVDFCGKGYH LM SFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNTFVSGNCD VVI GIVNNT VYDPLQPELD SFKEELDKYF KNHTSPDVDL GDISGINASV VNIQKEIDRL NEVAKNLNES LIDLQELGKY EQGS GYIPE APRDGQAYVR KDGEWVLLST FLGRSLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSAWSHPQ FEK

UniProtKB: Spike glycoprotein, Fibritin

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Macromolecule #2: Heavy chain of R1-26 Fab

MacromoleculeName: Heavy chain of R1-26 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.908293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSLILLFL VAVATRVLSE VQLVESGGGL VQPGGSLRLS CAASGFTFSS YWMSWVRQAP GKGLEWVANI KQDGSEKYYV DSVKGRFTI SRDNAKNSLY LQMNSLRAED TAVYYCARGQ LGPWVGVDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG G TAALGCLV ...String:
MGWSLILLFL VAVATRVLSE VQLVESGGGL VQPGGSLRLS CAASGFTFSS YWMSWVRQAP GKGLEWVANI KQDGSEKYYV DSVKGRFTI SRDNAKNSLY LQMNSLRAED TAVYYCARGQ LGPWVGVDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG G TAALGCLV KDYFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PK SCD

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Macromolecule #3: Light chain of R1-26 Fab

MacromoleculeName: Light chain of R1-26 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.558242 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVNFM LTQPHSVSES PGKTVTISCT GSSGSIASNY VQWYQQRPGS APTTVIYEDN QRPSGVPDRF SGSIDSSSN SASLTISGLK TEDEADYYCQ SYDSSNWVFG GGTQLTVLGT KLTVLGQPKA APSVTLFPPS SEELQANKAT L VCLISDFY ...String:
MGWSCIILFL VATATGVNFM LTQPHSVSES PGKTVTISCT GSSGSIASNY VQWYQQRPGS APTTVIYEDN QRPSGVPDRF SGSIDSSSN SASLTISGLK TEDEADYYCQ SYDSSNWVFG GGTQLTVLGT KLTVLGQPKA APSVTLFPPS SEELQANKAT L VCLISDFY PGAVTVAWKA DSSPVKAGVE TTTPSKQSNN KYAASSYLSL TPEQWKSHRS YSCQVTHEGS TVEKTVAPTE CS

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 60 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7yeg


Details: Heavy chain of R1-26 was started from 5X8M. Light chain of R1-26 was started from 7D6I
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 43870
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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