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- PDB-7mzi: SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 -

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Basic information

Entry
Database: PDB / ID: 7mzi
TitleSARS-CoV-2 receptor binding domain bound to Fab WCSL 129
Components
  • Spike protein S1
  • WCSL 129 heavy chain
  • WCSL 129 light chain
KeywordsVIRAL PROTEIN / SARS-CoV-2 / spike / RBD / human antibody
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, 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-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, 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, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPymm, P. / Tan, L.L. / Dietrich, M.H. / Chan, L.J. / Tham, W.H.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT2002073 Australia
CitationJournal: Cell Rep / Year: 2021
Title: Landscape of human antibody recognition of the SARS-CoV-2 receptor binding domain.
Authors: Adam K Wheatley / Phillip Pymm / Robyn Esterbauer / Melanie H Dietrich / Wen Shi Lee / Damien Drew / Hannah G Kelly / Li-Jin Chan / Francesca L Mordant / Katrina A Black / Amy Adair / Hyon- ...Authors: Adam K Wheatley / Phillip Pymm / Robyn Esterbauer / Melanie H Dietrich / Wen Shi Lee / Damien Drew / Hannah G Kelly / Li-Jin Chan / Francesca L Mordant / Katrina A Black / Amy Adair / Hyon-Xhi Tan / Jennifer A Juno / Kathleen M Wragg / Thakshila Amarasena / Ester Lopez / Kevin J Selva / Ebene R Haycroft / James P Cooney / Hariprasad Venugopal / Li Lynn Tan / Matthew T O Neill / Cody C Allison / Deborah Cromer / Miles P Davenport / Richard A Bowen / Amy W Chung / Marc Pellegrini / Mark T Liddament / Alisa Glukhova / Kanta Subbarao / Stephen J Kent / Wai-Hong Tham /
Abstract: Potent neutralizing monoclonal antibodies are one of the few agents currently available to treat COVID-19. SARS-CoV-2 variants of concern (VOCs) that carry multiple mutations in the viral spike ...Potent neutralizing monoclonal antibodies are one of the few agents currently available to treat COVID-19. SARS-CoV-2 variants of concern (VOCs) that carry multiple mutations in the viral spike protein can exhibit neutralization resistance, potentially affecting the effectiveness of some antibody-based therapeutics. Here, the generation of a diverse panel of 91 human, neutralizing monoclonal antibodies provides an in-depth structural and phenotypic definition of receptor binding domain (RBD) antigenic sites on the viral spike. These RBD antibodies ameliorate SARS-CoV-2 infection in mice and hamster models in a dose-dependent manner and in proportion to in vitro, neutralizing potency. Assessing the effect of mutations in the spike protein on antibody recognition and neutralization highlights both potent single antibodies and stereotypic classes of antibodies that are unaffected by currently circulating VOCs, such as B.1.351 and P.1. These neutralizing monoclonal antibodies and others that bind analogous epitopes represent potentially useful future anti-SARS-CoV-2 therapeutics.
History
DepositionMay 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 27, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: WCSL 129 light chain
H: WCSL 129 heavy chain
A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,46319
Polymers69,3933
Non-polymers2,07016
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-22 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.562, 71.896, 113.688
Angle α, β, γ (deg.)90.000, 108.320, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody WCSL 129 light chain


Mass: 22751.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody WCSL 129 heavy chain


Mass: 23568.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules A

#3: Protein Spike protein S1


Mass: 23073.766 Da / Num. of mol.: 1 / Fragment: Receptor Binding Domain (RBD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 441 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 18% PEG3350, 0.1 M tri sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.85→44.55 Å / Num. obs: 69190 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.049 / Rrim(I) all: 0.093 / Net I/σ(I): 9.6 / Num. measured all: 243523 / Scaling rejects: 2
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
1.85-1.893.60.8221519142300.680.5040.9661.698.6
9.06-44.553.40.02621296180.9990.0160.03132.797.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIXdev_3965refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41

6w41


Resolution: 1.85→44.55 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2075 3616 5.23 %
Rwork0.174 65558 -
obs0.1758 69174 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.65 Å2 / Biso mean: 35.2505 Å2 / Biso min: 13 Å2
Refinement stepCycle: final / Resolution: 1.85→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 168 426 5315
Biso mean--65.96 38.95 -
Num. residues----628
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.870.30721370.28152484262199
1.87-1.90.28631390.25362486262598
1.9-1.930.27061100.24362526263699
1.93-1.960.25761360.22972487262399
1.96-1.990.27651440.22642502264699
1.99-2.020.26051600.22382445260599
2.02-2.050.25541440.21522546269098
2.05-2.090.26211350.202324942629100
2.09-2.130.2691360.19992501263799
2.13-2.170.25831330.18872535266899
2.17-2.220.23161190.184325112630100
2.22-2.270.22231320.18242518265099
2.27-2.330.21781360.18742526266299
2.33-2.390.23451250.19062526265199
2.39-2.460.26361220.190925522674100
2.46-2.540.25331560.1922508266499
2.54-2.630.27091290.196225202649100
2.63-2.740.23981590.192525532712100
2.74-2.860.21381350.18112502263799
2.86-3.020.20811230.172625312654100
3.02-3.20.21311510.177625432694100
3.2-3.450.21161430.161725412684100
3.45-3.80.1811350.155725582693100
3.8-4.350.14881590.142725372696100
4.35-5.480.16261520.125625472699100
5.48-44.550.16151660.15792579274599

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