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- PDB-7cwo: SARS-CoV-2 spike protein RBD and P17 fab complex -

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Basic information

Entry
Database: PDB / ID: 7cwo
TitleSARS-CoV-2 spike protein RBD and P17 fab complex
Components
  • Spike glycoproteinPeplomer
  • heavy chain of P17 Fab
  • light chain of P17 Fab
KeywordsVIRAL PROTEIN / Complex / Fab / SARS-CoV-2 spike protein
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
Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Spike glycoprotein, heptad repeat 2, coronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Spike glycoprotein S2 superfamily, coronavirus / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding
Spike glycoprotein
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWang, X. / Wang, N.
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 Report
SummaryFull reportAbout validation report
History
DepositionAug 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Assembly

Deposited unit
A: Spike glycoprotein
H: heavy chain of P17 Fab
L: light chain of P17 Fab


Theoretical massNumber of molelcules
Total (without water)166,0863
Polymers166,0863
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3430 Å2
ΔGint-22 kcal/mol
Surface area19520 Å2

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Components

#1: Protein Spike glycoprotein / Peplomer / S glycoprotein / E2 / Peplomer protein


Mass: 141297.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody heavy chain of P17 Fab


Mass: 13165.724 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody light chain of P17 Fab


Mass: 11622.839 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Local reconstruction of SARS-CoV-2 spike protein and P17 Fab complex binding interfaceCOMPLEX#1-#30MULTIPLE SOURCES
2SARS-CoV-2 spike proteinCOMPLEX#11RECOMBINANT
3P17 FabCOMPLEX#2-#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Severe acute respiratory syndrome coronavirus 22697049
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
22Homo sapiens (human)9606HEK293
33Homo sapiens (human)9606HEK293
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249308 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0063354
ELECTRON MICROSCOPYf_angle_d0.9774566
ELECTRON MICROSCOPYf_dihedral_angle_d7.4772150
ELECTRON MICROSCOPYf_chiral_restr0.057495
ELECTRON MICROSCOPYf_plane_restr0.007588

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