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- PDB-6xcm: Structure of the SARS-CoV-2 spike glycoprotein in complex with th... -

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Basic information

Entry
Database: PDB / ID: 6xcm
TitleStructure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 1)
Components
  • C105 Fab Heavy Chain
  • C105 Fab Light Chain
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Spike glycoprotein / COVID-19 / monoclonal neutralizing antibody / Fabs / nsEMPEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / host cell surface receptor binding / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane
Spike glycoprotein S2, coronavirus / Spike receptor binding domain, betacoronavirus / Spike glycoprotein, heptad repeat 2, coronavirus / Spike receptor binding domain superfamily, coronavirus
Spike glycoprotein
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsBarnes, C.O. / Bjorkman, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-AI138398-S1 United States
CitationJournal: bioRxiv / Year: 2020
Title: Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies.
Authors: Christopher O Barnes / Anthony P West / Kathryn E Huey-Tubman / Magnus A G Hoffmann / Naima G Sharaf / Pauline R Hoffman / Nicholas Koranda / Harry B Gristick / Christian Gaebler / Frauke ...Authors: Christopher O Barnes / Anthony P West / Kathryn E Huey-Tubman / Magnus A G Hoffmann / Naima G Sharaf / Pauline R Hoffman / Nicholas Koranda / Harry B Gristick / Christian Gaebler / Frauke Muecksch / Julio C Cetrulo Lorenzi / Shlomo Finkin / Thomas Hagglof / Arlene Hurley / Katrina G Millard / Yiska Weisblum / Fabian Schmidt / Theodora Hatziioannou / Paul D Bieniasz / Marina Caskey / Davide F Robbiani / Michel C Nussenzweig / Pamela J Bjorkman /
Abstract: Neutralizing antibody responses to coronaviruses focus on the trimeric spike, with most against the receptor-binding domain (RBD). Here we characterized polyclonal IgGs and Fabs from COVID-19 ...Neutralizing antibody responses to coronaviruses focus on the trimeric spike, with most against the receptor-binding domain (RBD). Here we characterized polyclonal IgGs and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their degree of focus on RBD epitopes, recognition of SARS-CoV, MERS-CoV, and mild coronaviruses, and how avidity effects contributed to increased binding/neutralization of IgGs over Fabs. Electron microscopy reconstructions of polyclonal plasma Fab-spike complexes showed recognition of both S1 and RBD epitopes. A 3.4Å cryo-EM structure of a neutralizing monoclonal Fab-S complex revealed an epitope that blocks ACE2 receptor-binding on "up" RBDs. Modeling suggested that IgGs targeting these sites have different potentials for inter-spike crosslinking on viruses and would not be greatly affected by identified SARS-CoV-2 spike mutations. These studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from and similarity to a SARS-CoV antibody, providing criteria for evaluating vaccine-elicited antibodies.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release

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Structure visualization

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  • EMDB-22127
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
H: C105 Fab Heavy Chain
N: C105 Fab Heavy Chain
L: C105 Fab Light Chain
S: C105 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)527,31766
Polymers514,4787
Non-polymers12,83959
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area43820 Å2
ΔGint-11 kcal/mol
Surface area149370 Å2

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 139788.953 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 / Plasmid: pCAGGS / Cell line (production host): HeLa / Production host: Homo sapiens (human) / Strain (production host): Expi293F / References: UniProt: P0DTC2

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Antibody , 2 types, 4 molecules HNLS

#2: Antibody C105 Fab Heavy Chain


Mass: 24662.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: p3BNC / Cell line (production host): HeLa / Production host: Homo sapiens (human) / Strain (production host): Expi293F
#3: Antibody C105 Fab Light Chain


Mass: 22893.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: p3BNC / Cell line (production host): HeLa / Production host: Homo sapiens (human) / Strain (production host): Expi293F

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Sugars , 3 types, 59 molecules

#4: Sugar...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 55
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
#5: Sugar ChemComp-FUC / ALPHA-L-FUCOSE / Fucose


Mass: 164.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
#6: Sugar ChemComp-BMA / BETA-D-MANNOSE / Mannose


Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6

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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 S 2P trimer complexed with monoclonal Fab fragments from neutralizing antibody C105COMPLEX1, 2, 30MULTIPLE SOURCES
2SARS-CoV-2 spike glycoprotein 2P trimerCOMPLEX11RECOMBINANT
3neutralizing antibody C105 FabCOMPLEX2, 31RECOMBINANT
Molecular weightValue: 0.7 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Severe acute respiratory syndrome coronavirus 22697049
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCellPlasmid
12Homo sapiens (human)9606Expi293FHeLapCAGGS
23Homo sapiens (human)9606Expi293FHeLap3BNC
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaClSodium chloride1
220 mMTris-HClTris1
SpecimenConc.: 1.5 mg/ml
Details: Monodisperse sample taken after size-exclusion chromatography
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 60 s glow discharge in air at 0.20 mA current / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: 3 microliters added, blotted for 3 s with 0 blot force

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Collected with 3x3 pattern and beam image shift
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.89 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5940

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
7UCSF Chimeramodel fitting
9cryoSPARC2.14.2initial Euler assignment
10cryoSPARC2.14.2final Euler assignment
11cryoSPARC2.14.2classification
12cryoSPARC2.14.23D reconstruction
13PHENIX1.17model refinement
Image processingDetails: Gain-normalized and collected in counting mode with 40 frames per movie
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58873 / Symmetry type: POINT
Atomic model buildingB value: 90 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 6VYB
Pdb chain-ID: B
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00827358
ELECTRON MICROSCOPYf_angle_d0.68837250
ELECTRON MICROSCOPYf_dihedral_angle_d10.5293987
ELECTRON MICROSCOPYf_chiral_restr0.0474443
ELECTRON MICROSCOPYf_plane_restr0.0044714

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