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- PDB-6xca: Crystal structure of an anti-SARS-CoV-2 human neutralizing antibo... -

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Basic information

Entry
Database: PDB / ID: 6xca
TitleCrystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C105
Components
  • C105 Heavy Chain
  • C105 Light Chain
KeywordsIMMUNE SYSTEM / Antibody / SARS-CoV-2 / SARS2 / Coronavirus / Neutralizing
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSharaf, N.G. / Barnes, 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: Cell / 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 Hägglöf / 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 mainly target the receptor-binding domain (RBD) of the trimeric spike. Here, we characterized polyclonal immunoglobulin Gs (IgGs) and Fabs from COVID- ...Neutralizing antibody responses to coronaviruses mainly target the receptor-binding domain (RBD) of the trimeric spike. Here, we characterized polyclonal immunoglobulin Gs (IgGs) and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their focus on RBD epitopes, recognition of alpha- and beta-coronaviruses, and contributions of avidity to increased binding/neutralization of IgGs over Fabs. Using electron microscopy, we examined specificities of polyclonal plasma Fabs, revealing recognition of both S1 and RBD epitopes on SARS-CoV-2 spike. Moreover, a 3.4 Å cryo-electron microscopy (cryo-EM) structure of a neutralizing monoclonal Fab-spike complex revealed an epitope that blocks ACE2 receptor binding. Modeling based on these structures suggested different potentials for inter-spike crosslinking by IgGs on viruses, and characterized IgGs would not be affected by identified SARS-CoV-2 spike mutations. Overall, our studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.
History
DepositionJun 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: C105 Heavy Chain
L: C105 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7064
Polymers47,5142
Non-polymers1922
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-47 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.413, 120.081, 123.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11H-549-

HOH

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Components

#1: Antibody C105 Heavy Chain


Mass: 24634.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: p3BNC / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody C105 Light Chain


Mass: 22879.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: p3BNC / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 150 mM lithium sulfate, 100 mM citric acid, pH 3.5, 18% v/v PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→38.89 Å / Num. obs: 46713 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.079 / Rrim(I) all: 0.208 / Net I/σ(I): 5.7 / Num. measured all: 318966 / Scaling rejects: 901
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.846.51.6821796127520.5410.7051.8271.299.8
9-38.896.20.07426654280.9950.0310.0811.398.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3U36

3u36


Resolution: 1.8→38.89 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 2320 4.97 %
Rwork0.186 44362 -
obs0.1874 46682 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.69 Å2 / Biso mean: 27.1921 Å2 / Biso min: 12.09 Å2
Refinement stepCycle: final / Resolution: 1.8→38.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 10 479 3632
Biso mean--24.37 35.93 -
Num. residues----422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.30931330.30632576270999
1.84-1.880.26451270.256525992726100
1.88-1.920.2821460.222125672713100
1.92-1.970.24121290.211125832712100
1.97-2.020.24671440.205725492693100
2.02-2.080.22541510.200525862737100
2.08-2.150.19911410.190925962737100
2.15-2.220.22741190.184825832702100
2.23-2.310.23171590.192925792738100
2.31-2.420.28391500.191725772727100
2.42-2.550.25011220.204926042726100
2.55-2.710.24561270.203826412768100
2.71-2.920.27881150.201626132728100
2.92-3.210.22161300.192726352765100
3.21-3.670.19921400.168226302770100
3.67-4.630.15341350.146726722807100
4.63-38.890.1691520.169727722924100

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