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- PDB-7r6w: SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2... -

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Basic information

Entry
Database: PDB / ID: 7r6w
TitleSARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2X35 Fab and S309 Fab
Components
  • (Heavy Chain of Fab domain of monoclonal antibody ...) x 2
  • (Light Chain of Fab domain of monoclonal antibody ...) x 2
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / COVID-19 / SARS-CoV-2 / neutralizing monoclonal antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
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
N-PROPANOL / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsSnell, G. / Czudnochowski, N. / Hernandez, P. / Nix, J.C. / Croll, T.I. / Corti, D. / Cameroni, E. / Pinto, D. / Beltramello, M.
CitationJournal: Nature / Year: 2021
Title: SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape.
Authors: Tyler N Starr / Nadine Czudnochowski / Zhuoming Liu / Fabrizia Zatta / Young-Jun Park / Amin Addetia / Dora Pinto / Martina Beltramello / Patrick Hernandez / Allison J Greaney / Roberta ...Authors: Tyler N Starr / Nadine Czudnochowski / Zhuoming Liu / Fabrizia Zatta / Young-Jun Park / Amin Addetia / Dora Pinto / Martina Beltramello / Patrick Hernandez / Allison J Greaney / Roberta Marzi / William G Glass / Ivy Zhang / Adam S Dingens / John E Bowen / M Alejandra Tortorici / Alexandra C Walls / Jason A Wojcechowskyj / Anna De Marco / Laura E Rosen / Jiayi Zhou / Martin Montiel-Ruiz / Hannah Kaiser / Josh R Dillen / Heather Tucker / Jessica Bassi / Chiara Silacci-Fregni / Michael P Housley / Julia di Iulio / Gloria Lombardo / Maria Agostini / Nicole Sprugasci / Katja Culap / Stefano Jaconi / Marcel Meury / Exequiel Dellota / Rana Abdelnabi / Shi-Yan Caroline Foo / Elisabetta Cameroni / Spencer Stumpf / Tristan I Croll / Jay C Nix / Colin Havenar-Daughton / Luca Piccoli / Fabio Benigni / Johan Neyts / Amalio Telenti / Florian A Lempp / Matteo S Pizzuto / John D Chodera / Christy M Hebner / Herbert W Virgin / Sean P J Whelan / David Veesler / Davide Corti / Jesse D Bloom / Gyorgy Snell /
Abstract: An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape, have activity against diverse sarbecoviruses, and be highly protective through viral neutralization and effector functions. ...An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape, have activity against diverse sarbecoviruses, and be highly protective through viral neutralization and effector functions. Understanding how these properties relate to each other and vary across epitopes would aid the development of therapeutic antibodies and guide vaccine design. Here we comprehensively characterize escape, breadth and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD). Despite a trade-off between in vitro neutralization potency and breadth of sarbecovirus binding, we identify neutralizing antibodies with exceptional sarbecovirus breadth and a corresponding resistance to SARS-CoV-2 escape. One of these antibodies, S2H97, binds with high affinity across all sarbecovirus clades to a cryptic epitope and prophylactically protects hamsters from viral challenge. Antibodies that target the angiotensin-converting enzyme 2 (ACE2) receptor-binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency. Nevertheless, we also characterize a potent RBM antibody (S2E12) with breadth across sarbecoviruses related to SARS-CoV-2 and a high barrier to viral escape. These data highlight principles underlying variation in escape, breadth and potency among antibodies that target the RBD, and identify epitopes and features to prioritize for therapeutic development against the current and potential future pandemics.
History
DepositionJun 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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
B: Light Chain of Fab domain of monoclonal antibody S309
A: Heavy Chain of Fab domain of monoclonal antibody S309
L: Light Chain of Fab domain of monoclonal antibody S2X35
H: Heavy Chain of Fab domain of monoclonal antibody S2X35
R: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,08237
Polymers119,9465
Non-polymers3,13732
Water10,521584
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.267, 239.372, 129.806
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

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Antibody , 4 types, 4 molecules BALH

#1: Antibody Light Chain of Fab domain of monoclonal antibody S309


Mass: 23204.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 suspension / Production host: Homo sapiens (human)
#2: Antibody Heavy Chain of Fab domain of monoclonal antibody S309


Mass: 24573.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 suspension / Production host: Homo sapiens (human)
#3: Antibody Light Chain of Fab domain of monoclonal antibody S2X35


Mass: 22944.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 suspension / Production host: Homo sapiens (human)
#4: Antibody Heavy Chain of Fab domain of monoclonal antibody S2X35


Mass: 24780.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 suspension / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 2 molecules R

#5: Protein Spike protein S1


Mass: 24442.332 Da / Num. of mol.: 1 / Fragment: receptor-binding domain (UNP reisdues 328-531)
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)-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

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Non-polymers , 5 types, 615 molecules

#7: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL / Propan-1-ol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 3.56 Å3/Da / Density % sol: 65.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.85 M ammonium sulfate, 0.1 M Tris, pH 8.17, 0.8% w/v polyvinyl alcohol, 1% v/v 1-propanol, 0.01 M HEPES, pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.83→39.52 Å / Num. obs: 144449 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Net I/σ(I): 16.2 / Num. measured all: 974144
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
1.83-1.8672.964946271100.3061.2023.1990.799.5
10.02-39.526.50.014633497010.0060.01582.598.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSVERSION Jan 31, 2020 BUILT=20200417data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7JX3 and homology model of S2X35 Fab

7jx3


Resolution: 1.83→38.91 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.623 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 7049 4.9 %RANDOM
Rwork0.2113 ---
obs0.2123 135667 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.22 Å2 / Biso mean: 37.283 Å2 / Biso min: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å2-0 Å20 Å2
2---0.13 Å2-0 Å2
3----1.46 Å2
Refinement stepCycle: final / Resolution: 1.83→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8160 0 172 584 8916
Biso mean--75.47 42.94 -
Num. residues----1074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138516
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177659
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.65211617
X-RAY DIFFRACTIONr_angle_other_deg1.1541.57917714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3451068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75722.842366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.067151285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8471534
X-RAY DIFFRACTIONr_chiral_restr0.0460.21111
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021924
LS refinement shellResolution: 1.83→1.877 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 443 -
Rwork0.372 9502 -
all-9945 -
obs--93.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4267-0.2568-0.14380.88021.20742.90010.0364-0.04390.0208-0.0592-0.006-0.0508-0.2120.0076-0.03040.0848-0.04930.00080.0364-0.00740.1158-73.69236.621104.627
20.4336-0.1926-0.28641.03761.38023.0517-0.0136-0.0913-0.01220.2122-0.10460.10220.2196-0.18370.11820.1197-0.04880.02790.0743-0.01710.1336-85.22622.185103.762
32.56760.163-0.08651.4570.03570.8809-0.02960.04190.085-0.0028-0.0130.1409-0.0004-0.06440.04270.12310.0213-0.01620.0092-0.00570.0193-69.55814.57957.798
40.46660.4567-0.39092.2757-0.97680.66380.00030.05670.0584-0.188-0.0078-0.12450.06430.04760.00750.0890.0579-0.01740.0845-0.00480.1049-55.91546.85826.599
50.56810.5733-0.30932.8873-1.60271.51060.05530.01220.09360.0739-0.00720.0815-0.09890.0235-0.04810.05810.0418-0.01070.0408-0.00670.1019-69.13854.9633.411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 213
2X-RAY DIFFRACTION2A1 - 228
3X-RAY DIFFRACTION3R333 - 527
4X-RAY DIFFRACTION4L2 - 216
5X-RAY DIFFRACTION5H1 - 230

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