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- EMDB-33049: Cryo-EM structure of SARS-CoV spike protein in complex with three... -

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Basic information

Entry
Database: EMDB / ID: EMD-33049
TitleCryo-EM structure of SARS-CoV spike protein in complex with three nAbs X01, X10 and X17
Map data
Sample
  • Complex: Cryo-EM structure of SARS-CoV spike protein in complex with three nAbs X01, X10 and X17
    • Complex: nAbs X01, X10 and X17
      • Protein or peptide: X10 light chain
      • Protein or peptide: X10 heavy chain
      • Protein or peptide: X17 light chain
      • Protein or peptide: X17 heavy chain
      • Protein or peptide: X01 light chain
      • Protein or peptide: X01 heavy chain
    • Complex: SARS-CoV spike protein
      • Protein or peptide: Spike protein S1
KeywordsSARS-CoV-2 / Neutralizing antibody / Cryo-EM / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / 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 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse) / Severe acute respiratory syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsSun H / Liu L / Zhang T / Zheng Q / Li S / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: The neutralizing breadth of antibodies targeting diverse conserved epitopes between SARS-CoV and SARS-CoV-2.
Authors: Hualong Xiong / Hui Sun / Siling Wang / Lunzhi Yuan / Liqin Liu / Yuhe Zhu / Jinlei Zhang / Yang Huang / Ruoyao Qi / Yao Jiang / Jian Ma / Ming Zhou / Yue Ma / Rao Fu / Siping Yan / Mingxi ...Authors: Hualong Xiong / Hui Sun / Siling Wang / Lunzhi Yuan / Liqin Liu / Yuhe Zhu / Jinlei Zhang / Yang Huang / Ruoyao Qi / Yao Jiang / Jian Ma / Ming Zhou / Yue Ma / Rao Fu / Siping Yan / Mingxi Yue / Yangtao Wu / Min Wei / Yizhen Wang / Tingting Li / Yingbin Wang / Zizheng Zheng / Hai Yu / Tong Cheng / Shaowei Li / Quan Yuan / Jun Zhang / Yi Guan / Qingbing Zheng / Tianying Zhang / Ningshao Xia /
Abstract: Antibody therapeutics for the treatment of COVID-19 have been highly successful. However, the recent emergence of the Omicron variant has posed a challenge, as it evades detection by most existing ...Antibody therapeutics for the treatment of COVID-19 have been highly successful. However, the recent emergence of the Omicron variant has posed a challenge, as it evades detection by most existing SARS-CoV-2 neutralizing antibodies (nAbs). Here, we successfully generated a panel of SARS-CoV-2/SARS-CoV cross-neutralizing antibodies by sequential immunization of the two pseudoviruses. Of the potential candidates, we found that nAbs X01, X10, and X17 offer broad neutralizing potential against most variants of concern, with X17 further identified as a Class 5 nAb with undiminished neutralization against the Omicron variant. Cryo-electron microscopy structures of the three antibodies together in complex with each of the spike proteins of the prototypical SARS-CoV, SARS-CoV-2, and Delta and Omicron variants of SARS-CoV-2 defined three nonoverlapping conserved epitopes on the receptor-binding domain. The triple-antibody mixture exhibited enhanced resistance to viral evasion and effective protection against infection of the Beta variant in hamsters. Our findings will aid the development of antibody therapeutics and broad vaccines against SARS-CoV-2 and its emerging variants.
History
DepositionMar 10, 2022-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33049.png

Downloads & links

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Map

FileDownload / File: emd_33049.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 576 pix.
= 448.128 Å		0.78 Å/pix.
x 576 pix.
= 448.128 Å		0.78 Å/pix.
x 576 pix.
= 448.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.45899153 - 0.75529337
Average (Standard dev.)-0.00010051761 (±0.010133189)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 448.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of SARS-CoV spike protein in complex with three...

EntireName: Cryo-EM structure of SARS-CoV spike protein in complex with three nAbs X01, X10 and X17
Components
  • Complex: Cryo-EM structure of SARS-CoV spike protein in complex with three nAbs X01, X10 and X17
    • Complex: nAbs X01, X10 and X17
      • Protein or peptide: X10 light chain
      • Protein or peptide: X10 heavy chain
      • Protein or peptide: X17 light chain
      • Protein or peptide: X17 heavy chain
      • Protein or peptide: X01 light chain
      • Protein or peptide: X01 heavy chain
    • Complex: SARS-CoV spike protein
      • Protein or peptide: Spike protein S1

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Supramolecule #1: Cryo-EM structure of SARS-CoV spike protein in complex with three...

SupramoleculeName: Cryo-EM structure of SARS-CoV spike protein in complex with three nAbs X01, X10 and X17
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: nAbs X01, X10 and X17

SupramoleculeName: nAbs X01, X10 and X17 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: SARS-CoV spike protein

SupramoleculeName: SARS-CoV spike protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Severe acute respiratory syndrome coronavirus

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Macromolecule #1: X10 light chain

MacromoleculeName: X10 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.10242 KDa
SequenceString:
DIVLTQSPAS LAVSLGQRAA ISCRASQSVS TSSHNYVHWY QQRPGQPPKL LIKYASNLEC GVPARFSGSG SGTDFTLNIH PVEEEDSAA YYCQHSWEIP YTFGGGTKLE IK

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Macromolecule #2: X10 heavy chain

MacromoleculeName: X10 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.396729 KDa
SequenceString:
EVQLQQSGPE LVKPGASVKI SCKTSGYTFT EYTLHWVKQS HGKSLEWIGG FDPNFGGATY NLKFEDKATL TVDKSSNTAY MELRSLTSE DSAVFYCARG DYGTSYAYFD FWGQGTTLTV SS

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Macromolecule #3: X17 light chain

MacromoleculeName: X17 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.77098 KDa
SequenceString:
DIQMTQTTSS LSASLGDRVT ISCRASQDIS NYLNWYQQKP DGTVKLLIYY TSRLHSGVPS RFSGSGSGTD YSLTISNLEQ EDIATYFCQ QGTTLPYTFG GGTKLEIK

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Macromolecule #4: X17 heavy chain

MacromoleculeName: X17 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.154423 KDa
SequenceString:
QVQLQQSGAE LARPGASVKL SCKASGYTFT FYWMQWLKQR PGQGLEWIGA IYPGDGDTRY TQRFKDKATL TADKSSSTAY IQLSSLASE DSAVYYCAGG EYDNYGFDYW GQGTTLTVSS

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Macromolecule #5: X01 light chain

MacromoleculeName: X01 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.783128 KDa
SequenceString:
DIQMTQSSSY LSVSLGGRVT ITCKASDHIN NWLAWYQQKP GNAPRLLISG VTNLETGVPS RFSGSGSGKN FTLSIASLQT EDVATYYCQ QYWSFPWTFG GGTKLEIR

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Macromolecule #6: X01 heavy chain

MacromoleculeName: X01 heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.057389 KDa
SequenceString:
EIQLQQSGPE LVAPGASVKV SCKASGYAFT SYNMYWVRQS HGKSLEWIGY IVPYNGGTTY NQEFKGKATL TVDKSSNTAY IHLNSLTSE DSAVYYCAKE GTYYGYDGVL ADWGQGTLVT

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Macromolecule #7: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Molecular weightTheoretical: 21.431129 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TNLCPFGEVF NATKFPSVYA WERKKISNCV ADYSVLYNST FFSTFKCYGV SATKLNDLCF SNVYADSFVV KGDDVRQIAP GQTGVIADY NYKLPDDFMG CVLAWNTRNI DATSTGNYNY KYRYLRHGKL RPFERDISNV PFSPDGKPCT PPALNCYWPL N DYGFYTTT GIGYQPYRVV VLSFELLNAP A

UniProtKB: Spike glycoprotein

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 230838
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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