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- PDB-7cws: SARS-CoV-2 Spike Proteins Trimer in Complex with FC05 and H014 Fa... -

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Basic information

Entry
Database: PDB / ID: 7cws
TitleSARS-CoV-2 Spike Proteins Trimer in Complex with FC05 and H014 Fabs Cocktail
Components
  • (Heavy Chain of ...) x 2
  • (Light Chain of ...) x 2
  • Spike glycoproteinPeplomer
KeywordsVIRAL 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 / Spike glycoprotein S2 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 S1, C-terminal / Spike receptor binding domain superfamily, coronavirus / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding
Spike glycoprotein / polysac:dglcpnacb1-4dglcpnacb1-roh:
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang, L. / Wang, X.
CitationJournal: Cell Res / Year: 2021
Title: Structure-based development of human antibody cocktails against SARS-CoV-2.
Authors: Nan Wang / Yao Sun / Rui Feng / Yuxi Wang / Yan Guo / Li Zhang / Yong-Qiang Deng / Lei Wang / Zhen Cui / Lei Cao / Yan-Jun Zhang / Weimin Li / Feng-Cai Zhu / Cheng-Feng Qin / Xiangxi Wang /
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 31, 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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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
L: Heavy Chain of FC05 Fab
C: Light Chain of FC05 Fab
D: Light Chain of H014 Fab
E: Heavy Chain of H014 Fab
F: Light Chain of H014 Fab
G: Heavy Chain of H014 Fab
H: Light Chain of H014 Fab
I: Heavy Chain of H014 Fab
N: Heavy Chain of FC05 Fab
K: Light Chain of FC05 Fab
P: Heavy Chain of FC05 Fab
M: Light Chain of FC05 Fab
O: Spike glycoprotein
Q: Spike glycoprotein
R: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)536,49446
Polymers526,58915
Non-polymers9,90531
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area54460 Å2
ΔGint-149 kcal/mol
Surface area202470 Å2

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Components

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Protein , 1 types, 3 molecules OQR

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


Mass: 125612.219 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

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Antibody , 4 types, 12 molecules LNPCKMDFHEGI

#1: Antibody Heavy Chain of FC05 Fab


Mass: 13289.744 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody Light Chain of FC05 Fab


Mass: 11231.378 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Antibody Light Chain of H014 Fab


Mass: 12010.525 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: Antibody Heavy Chain of H014 Fab


Mass: 13385.787 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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Sugars , 2 types, 31 molecules

#6: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN

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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
1SARS-CoV-2 spike proteins trimer in complex with FC05 and H014 fabs CocktailCOMPLEX#1-#50MULTIPLE SOURCES
2FC05 FabCOMPLEX#1-#21RECOMBINANT
3H014 FabCOMPLEX#3-#41RECOMBINANT
4SARS-CoV-2 spike proteinCOMPLEX#51RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
34Severe acute respiratory syndrome coronavirus 22697049
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
12Homo sapiens (human)9606HEK293T
23Homo sapiens (human)9606HEK293T
34Homo sapiens (human)9606HEK293T
Buffer solutionpH: 8
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99382 / Symmetry type: POINT

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