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- EMDB-30483: Complex of SARS-CoV-2 spike protein and Fab P17 with one RBD in o... -

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Basic information

Entry
Database: EMDB / ID: EMD-30483
TitleComplex of SARS-CoV-2 spike protein and Fab P17 with one RBD in open state and two RBD in closed state
Map data
SampleThe complex of SARS-CoV-2 spike protein and P17 with one RBD open and two RBDs closed:
SARS-CoV-2 spike protein / P17 / Spike glycoproteinPeplomer / P17 heavy chain / P17 light chain / ligand
Function / homology
Function and homology information


suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope ...suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein, heptad repeat 2, coronavirus / Spike glycoprotein S2, coronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal
Spike glycoprotein
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang N / Wang X
CitationJournal: Cell Res / Year: 2021
Title: Rational development of a human antibody cocktail that deploys multiple functions to confer Pan-SARS-CoVs protection.
Authors: Hangping Yao / Yao Sun / Yong-Qiang Deng / Nan Wang / Yongcong Tan / Na-Na Zhang / Xiao-Feng Li / Chao Kong / Yan-Peng Xu / Qi Chen / Tian-Shu Cao / Hui Zhao / Xintian Yan / Lei Cao / Zhe Lv ...Authors: Hangping Yao / Yao Sun / Yong-Qiang Deng / Nan Wang / Yongcong Tan / Na-Na Zhang / Xiao-Feng Li / Chao Kong / Yan-Peng Xu / Qi Chen / Tian-Shu Cao / Hui Zhao / Xintian Yan / Lei Cao / Zhe Lv / Dandan Zhu / Rui Feng / Nanping Wu / Wenhai Zhang / Yuhao Hu / Keda Chen / Rong-Rong Zhang / Qingyu Lv / Shihui Sun / Yunhua Zhou / Run Yan / Guan Yang / Xinglu Sun / Chanjuan Liu / Xiangyun Lu / Linfang Cheng / Hongying Qiu / Xing-Yao Huang / Tianhao Weng / Danrong Shi / Weidong Jiang / Junbin Shao / Lei Wang / Jie Zhang / Tao Jiang / Guojun Lang / Cheng-Feng Qin / Lanjuan Li / Xiangxi Wang /
Abstract: Structural principles underlying the composition and synergistic mechanisms of protective monoclonal antibody cocktails are poorly defined. Here, we exploited antibody cooperativity to develop a ...Structural principles underlying the composition and synergistic mechanisms of protective monoclonal antibody cocktails are poorly defined. Here, we exploited antibody cooperativity to develop a therapeutic antibody cocktail against SARS-CoV-2. On the basis of our previously identified humanized cross-neutralizing antibody H014, we systematically analyzed a fully human naive antibody library and rationally identified a potent neutralizing antibody partner, P17, which confers effective protection in animal model. Cryo-EM studies dissected the nature of the P17 epitope, which is SARS-CoV-2 specific and distinctly different from that of H014. High-resolution structure of the SARS-CoV-2 spike in complex with H014 and P17, together with functional investigations revealed that in a two-antibody cocktail, synergistic neutralization was achieved by S1 shielding and conformational locking, thereby blocking receptor attachment and viral membrane fusion, conferring high potency as well as robustness against viral mutation escape. Furthermore, cluster analysis identified a hypothetical 3rd antibody partner for further reinforcing the cocktail as pan-SARS-CoVs therapeutics.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionAug 29, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateJan 13, 2021-
Current statusJan 13, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cwm
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30483.png

Downloads & links

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Map

FileDownload / File: emd_30483.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 400 pix.
= 416. Å		1.04 Å/pix.
x 400 pix.
= 416. Å		1.04 Å/pix.
x 400 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00503 / Movie #1: 0.01
Minimum - Maximum-0.006313785 - 0.03899444
Average (Standard dev.)6.493042e-05 (±0.0011951324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0060.0390.000

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Supplemental data

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Sample components

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Entire The complex of SARS-CoV-2 spike protein and P17 with one RBD open...

EntireName: The complex of SARS-CoV-2 spike protein and P17 with one RBD open and two RBDs closed
Number of components: 7

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Component #1: protein, The complex of SARS-CoV-2 spike protein and P17 with one...

ProteinName: The complex of SARS-CoV-2 spike protein and P17 with one RBD open and two RBDs closed
Recombinant expression: No

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Component #2: protein, SARS-CoV-2 spike protein

ProteinName: SARS-CoV-2 spike protein / Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293

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Component #3: protein, P17

ProteinName: P17 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293

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Component #4: protein, Spike glycoprotein

ProteinName: Spike glycoproteinPeplomer / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 141.297422 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, P17 heavy chain

ProteinName: P17 heavy chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 13.165724 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, P17 light chain

ProteinName: P17 light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 11.622839 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: DARK FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 150376
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

7cwm

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