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- PDB-7mzk: SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab ... -

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Basic information

Entry
Database: PDB / ID: 7mzk
TitleSARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab PDI 96
Components
  • PDI 96 heavy chain
  • PDI 96 light chain
  • 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 / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / 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 / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPymm, P. / Dietrich, M.H. / Tan, L.L. / 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
Revision 1.4Nov 6, 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

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Assembly

Deposited unit
C: WCSL 129 heavy chain
B: Spike protein S1
E: WCSL 129 light chain
F: WCSL 129 heavy chain
A: Spike protein S1
N: PDI 96 heavy chain
M: PDI 96 light chain
H: PDI 96 heavy chain
L: PDI 96 light chain
D: WCSL 129 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,56717
Polymers235,83910
Non-polymers1,7287
Water14,358797
1
C: WCSL 129 heavy chain
B: Spike protein S1
N: PDI 96 heavy chain
M: PDI 96 light chain
D: WCSL 129 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7939
Polymers117,9205
Non-polymers8734
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: WCSL 129 light chain
F: WCSL 129 heavy chain
A: Spike protein S1
H: PDI 96 heavy chain
L: PDI 96 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7748
Polymers117,9205
Non-polymers8553
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.898, 103.561, 106.290
Angle α, β, γ (deg.)103.520, 101.820, 98.200
Int Tables number1
Space group name H-MP1

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Components

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Antibody , 4 types, 8 molecules CFEDNHML

#1: Antibody WCSL 129 heavy chain


Mass: 23568.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody WCSL 129 light chain


Mass: 22751.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody PDI 96 heavy chain


Mass: 24390.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody PDI 96 light chain


Mass: 24135.877 Da / Num. of mol.: 2
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, 4 molecules BA

#2: Protein Spike protein S1


Mass: 23073.766 Da / Num. of mol.: 2 / 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
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 802 molecules

#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Tri-sodium citrate pH 5.5, 10% PEG8000

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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: Jan 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.25→49.33 Å / Num. obs: 133496 / % possible obs: 98.2 % / Redundancy: 3.659 % / Biso Wilson estimate: 45.003 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.126 / Χ2: 0.833 / Net I/σ(I): 8.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.383.7260.7351.637899521904212020.670.85896.8
2.38-2.553.690.532.237472520689202500.7850.62197.9
2.55-2.753.5280.363.136654919233188620.8710.42698.1
2.75-3.013.6920.2215.196427717696174080.950.25898.4
3.01-3.373.7370.1318.635884915970157480.9830.15398.6
3.37-3.893.5460.08313.034932314103139110.9910.09898.6
3.89-4.753.6760.05819.094358611982118580.9950.06899
4.75-6.693.720.0552034034923291500.9960.06599.1
6.69-49.3263.5480.04125.4318120517851070.9980.04898.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MZI

7mzi


Resolution: 2.25→49.327 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 4004 3 %
Rwork0.1972 129428 -
obs0.1983 133432 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.69 Å2 / Biso mean: 50.4376 Å2 / Biso min: 17.36 Å2
Refinement stepCycle: final / Resolution: 2.25→49.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15836 0 158 797 16791
Biso mean--77.66 44.93 -
Num. residues----2130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.27650.4151340.3281434997
2.2765-2.30420.31551380.2973444398
2.3042-2.33340.31731360.279440498
2.3334-2.36410.29461380.2779446598
2.3641-2.39650.34031390.2672450498
2.3965-2.43070.28681350.2627433898
2.4307-2.4670.28351390.2549450698
2.467-2.50560.26151370.239442098
2.5056-2.54660.24131370.2398444098
2.5466-2.59050.31441390.2467449198
2.5905-2.63770.29211370.2476441298
2.6377-2.68840.2541370.2486445998
2.6884-2.74320.30651390.2391447798
2.7432-2.80290.26671380.2327446998
2.8029-2.86810.26591390.2222447798
2.8681-2.93980.25091370.2122443998
2.9398-3.01930.26451380.2177447199
3.0193-3.10810.26221390.2124448098
3.1081-3.20840.30961380.2103445999
3.2084-3.32310.26191400.2025452399
3.3231-3.45610.27821370.1941445699
3.4561-3.61330.23521390.1886449199
3.6133-3.80380.23471390.1838449699
3.8038-4.0420.19871380.1737446399
4.042-4.35390.1841390.1526449599
4.3539-4.79170.16551400.1414452899
4.7917-5.48430.17151390.1553448299
5.4843-6.90660.20551390.1854449799
6.9066-49.3270.19151400.171449499

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