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- PDB-7tty: Crystal structure of potent neutralizing antibody 10-40 in comple... -

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Basic information

Entry
Database: PDB / ID: 7tty
TitleCrystal structure of potent neutralizing antibody 10-40 in complex with bat WIV1 receptor-binding domain
Components
  • 1040 heavy chain
  • 1040 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / COVID-19 / SarbecoVirus / WIV1 RBD / Viral protein / Spike glycoprotein / Receptor Binding Protein / Neutralizing antibody / potent / 10-40 / Fab / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBat SARS-like coronavirus WIV1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsReddem, E.R. / Shapiro, L.
Funding support China, 1items
OrganizationGrant numberCountry
Jack Ma Foundation China
CitationJournal: Sci Transl Med / Year: 2022
Title: An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses.
Authors: Lihong Liu / Sho Iketani / Yicheng Guo / Eswar R Reddem / Ryan G Casner / Manoj S Nair / Jian Yu / Jasper F-W Chan / Maple Wang / Gabriele Cerutti / Zhiteng Li / Nicholas C Morano / Candace ...Authors: Lihong Liu / Sho Iketani / Yicheng Guo / Eswar R Reddem / Ryan G Casner / Manoj S Nair / Jian Yu / Jasper F-W Chan / Maple Wang / Gabriele Cerutti / Zhiteng Li / Nicholas C Morano / Candace D Castagna / Laura Corredor / Hin Chu / Shuofeng Yuan / Vincent Kwok-Man Poon / Chris Chun-Sing Chan / Zhiwei Chen / Yang Luo / Marcus Cunningham / Alejandro Chavez / Michael T Yin / David S Perlin / Moriya Tsuji / Kwok-Yung Yuen / Peter D Kwong / Zizhang Sheng / Yaoxing Huang / Lawrence Shapiro / David D Ho /
Abstract: The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related ...The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses, suggesting that 10-40 is a promising agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses but also uncovered a distinct antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine.
History
DepositionFeb 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: 1040 heavy chain
L: 1040 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1374
Polymers69,7133
Non-polymers4241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-13 kcal/mol
Surface area28270 Å2
Unit cell
Length a, b, c (Å)51.311, 69.546, 95.215
Angle α, β, γ (deg.)90.000, 105.631, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Spike protein S1


Mass: 21979.701 Da / Num. of mol.: 1 / Fragment: receptor-binding domain (UNP residues 322-515)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat SARS-like coronavirus WIV1 / Production host: Homo sapiens (human) / References: UniProt: U5WI05
#2: Antibody 1040 heavy chain


Mass: 24794.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 1040 light chain


Mass: 22938.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: 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.: 1
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
Has ligand of interestY
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate, pH 5.5, 20% propanol, 20% PEG4000

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.11→91.69 Å / Num. obs: 11493 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 79.5 Å2 / CC1/2: 0.943 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.165 / Rrim(I) all: 0.4 / Net I/σ(I): 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.19-3.416.91.7919300.3520.8010.999.8
8-106.60.2575240.9560.1070.27999.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7SD5

7sd5


Resolution: 3.11→91.69 Å / SU ML: 0.5979 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.8545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3293 1148 9.99 %
Rwork0.2346 10345 -
obs0.244 11493 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 3.11→91.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4854 0 28 0 4882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01545030
X-RAY DIFFRACTIONf_angle_d1.91656867
X-RAY DIFFRACTIONf_chiral_restr0.1036765
X-RAY DIFFRACTIONf_plane_restr0.0132877
X-RAY DIFFRACTIONf_dihedral_angle_d12.7724703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.250.3881250.31651082X-RAY DIFFRACTION82.73
3.25-3.420.36791460.31611316X-RAY DIFFRACTION98.98
3.42-3.630.39661460.28721324X-RAY DIFFRACTION99.86
3.64-3.920.35091450.2611313X-RAY DIFFRACTION99.86
3.92-4.310.32331440.22261306X-RAY DIFFRACTION98.17
4.31-4.930.28951460.18821318X-RAY DIFFRACTION99.93
4.93-6.210.3181490.21231329X-RAY DIFFRACTION100
6.22-100.32881470.24161357X-RAY DIFFRACTION98.82
Refinement TLS params.Method: refined / Origin x: 17.269 Å / Origin y: -3.966 Å / Origin z: 24.866 Å
111213212223313233
T0.736715964917 Å2-0.0393751223026 Å2-0.00706393274509 Å2-0.644163463301 Å20.075053836159 Å2--0.695323092954 Å2
L0.177802884874 °2-0.144697239426 °2-0.269273022737 °2-0.171865492611 °20.216553406814 °2--0.389223825776 °2
S-0.0860455459915 Å °0.00576995591222 Å °-0.081386239563 Å °0.0417402895934 Å °0.110296165592 Å °0.115617015725 Å °-0.163513827367 Å °0.0223881622179 Å °1.05281677308E-5 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 334:528 ) OR ( CHAIN H AND RESID 1:216 ) OR ( CHAIN L AND RESID 1:210 )A334 - 528
2X-RAY DIFFRACTION1( CHAIN A AND RESID 334:528 ) OR ( CHAIN H AND RESID 1:216 ) OR ( CHAIN L AND RESID 1:210 )H1 - 216
3X-RAY DIFFRACTION1( CHAIN A AND RESID 334:528 ) OR ( CHAIN H AND RESID 1:216 ) OR ( CHAIN L AND RESID 1:210 )L1 - 210

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