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- EMDB-30500: Binding interface of SARS-CoV-2 RBD and its neutralizing antibody HB27 -

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Basic information

Entry
Database: EMDB / ID: EMD-30500
TitleBinding interface of SARS-CoV-2 RBD and its neutralizing antibody HB27
Map data
Sample
  • Complex: Complex of SARS-CoV-2 RBD and its neutralizing antibody HB27
    • Complex: SARS-CoV-2 RBD
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: HB27 antibody
      • Protein or peptide: Light chain of HB27
      • Protein or peptide: Heavy chain of HB27
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, 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, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWang X / Zhu L
CitationJournal: Natl Sci Rev / Year: 2021
Title: Double lock of a potent human therapeutic monoclonal antibody against SARS-CoV-2.
Authors: Ling Zhu / Yong-Qiang Deng / Rong-Rong Zhang / Zhen Cui / Chun-Yun Sun / Chang-Fa Fan / Xiaorui Xing / Weijin Huang / Qi Chen / Na-Na Zhang / Qing Ye / Tian-Shu Cao / Nan Wang / Lei Wang / ...Authors: Ling Zhu / Yong-Qiang Deng / Rong-Rong Zhang / Zhen Cui / Chun-Yun Sun / Chang-Fa Fan / Xiaorui Xing / Weijin Huang / Qi Chen / Na-Na Zhang / Qing Ye / Tian-Shu Cao / Nan Wang / Lei Wang / Lei Cao / Huiyu Wang / Desheng Kong / Juan Ma / Chunxia Luo / Yanjing Zhang / Jianhui Nie / Yao Sun / Zhe Lv / Neil Shaw / Qianqian Li / Xiao-Feng Li / Junjie Hu / Liangzhi Xie / Zihe Rao / Youchun Wang / Xiangxi Wang / Cheng-Feng Qin /
Abstract: Receptor recognition and subsequent membrane fusion are essential for the establishment of successful infection by SARS-CoV-2. Halting these steps can cure COVID-19. Here we have identified and ...Receptor recognition and subsequent membrane fusion are essential for the establishment of successful infection by SARS-CoV-2. Halting these steps can cure COVID-19. Here we have identified and characterized a potent human monoclonal antibody, HB27, that blocks SARS-CoV-2 attachment to its cellular receptor at sub-nM concentrations. Remarkably, HB27 can also prevent SARS-CoV-2 membrane fusion. Consequently, a single dose of HB27 conferred effective protection against SARS-CoV-2 in two established mouse models. Rhesus macaques showed no obvious adverse events when administrated with 10 times the effective dose of HB27. Cryo-EM studies on complex of SARS-CoV-2 trimeric S with HB27 Fab reveal that three Fab fragments work synergistically to occlude SARS-CoV-2 from binding to the ACE2 receptor. Binding of the antibody also restrains any further conformational changes of the receptor binding domain, possibly interfering with progression from the prefusion to the postfusion stage. These results suggest that HB27 is a promising candidate for immuno-therapies against COVID-19.
History
DepositionSep 3, 2020-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateJun 9, 2021-
Current statusJun 9, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cyh
  • Surface level: 9
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7cyh
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_30500.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 9.0 / Movie #1: 9
Minimum - Maximum-31.455719 - 55.6176
Average (Standard dev.)0.20973003 (±1.4118552)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 209.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z210.000210.000210.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-288-288-288
NX/NY/NZ576576576
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-31.45655.6180.210

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Supplemental data

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Sample components

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Entire : Complex of SARS-CoV-2 RBD and its neutralizing antibody HB27

EntireName: Complex of SARS-CoV-2 RBD and its neutralizing antibody HB27
Components
  • Complex: Complex of SARS-CoV-2 RBD and its neutralizing antibody HB27
    • Complex: SARS-CoV-2 RBD
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: HB27 antibody
      • Protein or peptide: Light chain of HB27
      • Protein or peptide: Heavy chain of HB27

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Supramolecule #1: Complex of SARS-CoV-2 RBD and its neutralizing antibody HB27

SupramoleculeName: Complex of SARS-CoV-2 RBD and its neutralizing antibody HB27
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: SARS-CoV-2 RBD

SupramoleculeName: SARS-CoV-2 RBD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T

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Supramolecule #3: HB27 antibody

SupramoleculeName: HB27 antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 21.772391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL Q SYGFQPTN ...String:
NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL Q SYGFQPTN GVGYQPYRVV VLSFELLHAP ATVCGP

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Macromolecule #2: Light chain of HB27

MacromoleculeName: Light chain of HB27 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.921329 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IVLTQSPTLS LSPGERATLS CRASESVDNY GISFMNWFQQ KPGQAPRLLI YAASNQGSGI PSRFSGSGSG TDFSLTISSL EPEDFAVYF CQQSKEVPRI FGQGTKVEIL K

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Macromolecule #3: Heavy chain of HB27

MacromoleculeName: Heavy chain of HB27 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.917422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VKLVESGGGL VKPGGSLRLS CAASGFTFTN YGMSWVRQAP GKRLEWVAEI SSGGSYTYYP DTVTGRFTIS RDNAKNTLYL QMNSLRAED TAVYYCARFR YGGGGTVDYW GQGTLVTVSS

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 393321

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