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- PDB-7qf0: Crystal structure of the SARS-CoV-2 RBD in complex with the human... -

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Basic information

Entry
Database: PDB / ID: 7qf0
TitleCrystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.2325
Components
  • CV2.2325 heavy chain
  • CV2.2325 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / neutralization / antibody / coronavirus
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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFernandez, I. / Pederzoli, R. / Rey, F.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Exp Med / Year: 2022
Title: Potent human broadly SARS-CoV-2-neutralizing IgA and IgG antibodies effective against Omicron BA.1 and BA.2.
Authors: Cyril Planchais / Ignacio Fernández / Timothée Bruel / Guilherme Dias de Melo / Matthieu Prot / Maxime Beretta / Pablo Guardado-Calvo / Jérémy Dufloo / Luis M Molinos-Albert / Marija ...Authors: Cyril Planchais / Ignacio Fernández / Timothée Bruel / Guilherme Dias de Melo / Matthieu Prot / Maxime Beretta / Pablo Guardado-Calvo / Jérémy Dufloo / Luis M Molinos-Albert / Marija Backovic / Jeanne Chiaravalli / Emilie Giraud / Benjamin Vesin / Laurine Conquet / Ludivine Grzelak / Delphine Planas / Isabelle Staropoli / Florence Guivel-Benhassine / Thierry Hieu / Mikaël Boullé / Minerva Cervantes-Gonzalez / Marie-Noëlle Ungeheuer / Pierre Charneau / Sylvie van der Werf / Fabrice Agou / / / Jordan D Dimitrov / Etienne Simon-Lorière / Hervé Bourhy / Xavier Montagutelli / Félix A Rey / Olivier Schwartz / Hugo Mouquet /
Abstract: Memory B-cell and antibody responses to the SARS-CoV-2 spike protein contribute to long-term immune protection against severe COVID-19, which can also be prevented by antibody-based interventions. ...Memory B-cell and antibody responses to the SARS-CoV-2 spike protein contribute to long-term immune protection against severe COVID-19, which can also be prevented by antibody-based interventions. Here, wide SARS-CoV-2 immunoprofiling in Wuhan COVID-19 convalescents combining serological, cellular, and monoclonal antibody explorations revealed humoral immunity coordination. Detailed characterization of a hundred SARS-CoV-2 spike memory B-cell monoclonal antibodies uncovered diversity in their repertoire and antiviral functions. The latter were influenced by the targeted spike region with strong Fc-dependent effectors to the S2 subunit and potent neutralizers to the receptor-binding domain. Amongst those, Cv2.1169 and Cv2.3194 antibodies cross-neutralized SARS-CoV-2 variants of concern, including Omicron BA.1 and BA.2. Cv2.1169, isolated from a mucosa-derived IgA memory B cell demonstrated potency boost as IgA dimers and therapeutic efficacy as IgG antibodies in animal models. Structural data provided mechanistic clues to Cv2.1169 potency and breadth. Thus, potent broadly neutralizing IgA antibodies elicited in mucosal tissues can stem SARS-CoV-2 infection, and Cv2.1169 and Cv2.3194 are prime candidates for COVID-19 prevention and treatment.
History
DepositionDec 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: 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: CV2.2325 heavy chain
L: CV2.2325 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5008
Polymers70,9463
Non-polymers5545
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-51 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.565, 148.875, 145.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-729-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody CV2.2325 heavy chain


Mass: 24483.291 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 CV2.2325 light chain


Mass: 23394.012 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

#1: Protein Spike protein S1


Mass: 23068.695 Da / Num. of mol.: 1
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 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 , 3 types, 238 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M ammonium citrate (pH 7.0), 12% PEG 3350,

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9778 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.3→48.36 Å / Num. obs: 40972 / % possible obs: 99.9 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.041 / Rrim(I) all: 0.153 / Net I/σ(I): 17.4 / Num. measured all: 560786 / Scaling rejects: 836
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
2.3-2.3813.31.1885270439710.7690.3371.2362.499.7
8.91-48.3611.80.0493597920.9990.0120.04247.899.3

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J, 5I1E

6m0j

5i1e


Resolution: 2.3→42.8 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 2075 5.07 %
Rwork0.1849 38861 -
obs0.1867 40936 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.38 Å2 / Biso mean: 50.7921 Å2 / Biso min: 25.55 Å2
Refinement stepCycle: final / Resolution: 2.3→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4801 0 32 234 5067
Biso mean--91.5 48.2 -
Num. residues----625
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.350.29071280.26312526265499
2.35-2.410.28451240.244326012725100
2.41-2.480.29921210.25125662687100
2.48-2.550.25171430.246225572700100
2.55-2.630.29261650.232525242689100
2.63-2.730.28331760.216625212697100
2.73-2.840.22871250.211325882713100
2.84-2.960.251340.220825772711100
2.97-3.120.24951210.212925992720100
3.12-3.320.26291160.218225992715100
3.32-3.570.24281370.198526122749100
3.57-3.930.22371470.182925872734100
3.93-4.50.16071400.142126192759100
4.5-5.670.16541640.128926262790100
5.67-42.80.21231340.162327592893100
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)
10.79220.5957-0.06733.5025-1.71411.67760.4412-0.08360.35650.6956-0.02720.38-1.14610.21460.03790.6774-0.1398-0.01710.5091-0.07260.55311.990473.0442-11.8385
21.16481.2454-0.43353.4444-1.54321.95240.5670.19270.28050.9251-0.22570.1577-1.36390.3125-0.02270.4488-0.05830.06930.45250.04110.5844-2.888469.5319-17.5813
30.0768-0.59650.61947.817-7.58517.2151-0.14240.17720.21260.2901-0.5775-0.6796-0.97561.18820.48810.509-0.2142-0.0010.98850.00270.772714.034267.5738-15.6601
40.1247-0.2413-0.07432.8905-1.99172.0587-0.10520.26950.0322-0.1387-0.2701-0.3727-0.2850.30590.30370.4662-0.05410.0570.8263-0.00920.71759.404563.6191-25.3528
51.932-0.1313-0.12233.1254-1.3873.84060.04370.0740.08980.2946-0.0261-0.1719-0.310.13460.06550.3423-0.06670.04520.4603-0.03470.58420.694558.7701-11.655
60.87280.16880.09441.6056-0.98181.73150.11820.04040.0194-0.0806-0.1914-0.0232-0.3860.2350.04250.3579-0.03810.00730.4595-0.02110.49620.891756.2183-12.6854
71.5003-0.00550.02322.4804-1.78411.83580.2169-0.41310.06730.3331-0.220.4471-0.4795-0.061-0.06010.4666-0.04690.10080.4731-0.00360.5806-6.997756.2482-0.3926
80.58390.3128-0.1011.9895-0.22681.62430.06160.2402-0.1352-0.10580.34671.2029-0.1074-0.6709-0.22530.31540.02650.01980.46860.09970.7365-16.836652.4027-8.7432
90.0463-0.19130.19580.7338-0.49610.43290.2933-0.25520.05031.45020.11681.3201-0.0912-0.431-0.10260.42240.13080.23470.42450.0680.9305-18.533350.08722.6835
102.8529-0.8751.03292.1042-1.40751.057-0.0845-0.16550.18120.49710.0690.266-0.4540.10690.09860.6151-0.1189-0.02760.6031-0.01910.60824.623155.74823.9215
110.61060.4281-0.68242.7503-0.94913.47490.11590.33250.14740.01610.4210.1851-0.05380.09650.10710.3418-0.0718-0.01890.52340.07890.43042.810563.1529-14.4768
122.5419-1.78872.13322.2043-0.47174.15670.41350.1731-0.1124-0.1871-0.0773-0.2949-0.38280.4330.1230.7675-0.1490.01580.70560.09790.67511.700871.9203-32.2594
130.7203-0.21250.84953.4995-1.09071.1305-0.060.0562-0.12160.06440.0830.8190.2014-0.1279-0.08260.3671-0.0378-0.01920.33030.00710.5451-8.557521.2581-3.1884
140.0495-0.2178-0.38033.0911-0.40961.54040.04820.1381-0.07880.01840.05730.6949-0.0224-0.0687-0.14650.30570.0192-0.01570.3709-0.03260.543-7.262733.2888-3.4202
151.3571-0.9639-0.75453.1564-0.42642.44660.06230.4832-0.1663-0.6401-0.02420.49180.2717-0.1146-0.13280.33590.0124-0.09080.3901-0.02470.5464-6.934729.9979-9.7259
16-0.0497-0.62220.27182.7269-0.28481.9183-0.02370.03830.22360.14070.04080.34590.0693-0.001-0.12530.33850.00610.00690.3379-0.02660.5265-5.089230.17880.6771
171.0676-0.07230.26842.412-0.47681.71720.0395-0.0498-0.00080.1681-0.1806-0.12430.15050.1620.00630.3708-0.0149-0.00290.3542-0.01320.22817.90382.546112.559
180.6235-0.12190.79522.0527-1.15221.84650.1336-0.05960.08670.1382-0.14470.0060.12620.0221-0.0420.3768-0.00470.01020.4047-0.04870.18982.53963.32515.8813
191.2639-0.8684-0.09042.0731-0.59181.6333-0.0728-0.2869-0.01270.23570.0229-0.066-0.0179-0.1323-0.02340.3818-0.0295-0.00170.4078-0.05320.19064.78196.53919.5732
201.672-0.2146-0.20842.9561-1.27313.85060.0493-0.0996-0.16090.1110.0530.11680.5336-0.3434-0.24630.3577-0.05120.01280.4586-0.05720.2816-0.4428-2.84218.9343
213.12180.06991.47672.7296-0.94415.0325-0.0123-0.0282-0.84930.29970.2601-0.13260.37430.166-0.30170.4905-0.02260.02890.4168-0.03230.30244.237-6.523317.9607
220.90290.08740.62463.3649-1.96451.75720.0481-0.4260.05120.4623-0.46090.4306-0.40341.01670.06410.5779-0.05580.11260.5103-0.04480.52434.077336.737419.7726
230.9758-0.11450.53832.7885-1.472.56040.0129-0.17330.16050.7210.00690.3689-0.28750.1052-0.06180.56440.00520.13620.4131-0.12270.5433-3.623941.702615.2599
241.1343-0.23010.45572.7463-1.06691.87250.0934-0.1450.29350.5130.06450.4236-0.21540.1276-0.07340.4489-0.02660.08680.4063-0.10650.5303-1.73336.899512.683
251.4422-2.1460.80794.0324-2.11281.14860.20930.0890.6484-0.0585-0.0008-0.24640.0310.2095-0.03050.6501-0.00540.03050.5119-0.13230.49524.241924.545830.0196
261.9323-0.2067-0.00933.2983-0.02223.85740.05530.017-0.01780.5516-0.29970.00291.1302-0.17370.19210.4316-0.0072-0.01760.4607-0.03830.274315.8538-0.675418.6586
271.5448-0.5289-0.22462.0264-0.28211.80780.0478-0.04460.30970.3176-0.1181-0.2969-0.07930.17370.13050.4103-0.0259-0.04190.3833-0.04560.342517.409413.66921.0457
282.5433-1.5774-0.54812.81261.08241.82260.122-0.10640.08750.2547-0.1114-0.18160.04770.08020.13750.3851-0.0477-0.02780.395-0.00570.335817.54519.768623.5194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 334 through 349 )A334 - 349
2X-RAY DIFFRACTION2chain 'A' and (resid 350 through 364 )A350 - 364
3X-RAY DIFFRACTION3chain 'A' and (resid 365 through 375 )A365 - 375
4X-RAY DIFFRACTION4chain 'A' and (resid 376 through 393 )A376 - 393
5X-RAY DIFFRACTION5chain 'A' and (resid 394 through 409 )A394 - 409
6X-RAY DIFFRACTION6chain 'A' and (resid 410 through 442 )A410 - 442
7X-RAY DIFFRACTION7chain 'A' and (resid 443 through 459 )A443 - 459
8X-RAY DIFFRACTION8chain 'A' and (resid 460 through 479 )A460 - 479
9X-RAY DIFFRACTION9chain 'A' and (resid 480 through 494 )A480 - 494
10X-RAY DIFFRACTION10chain 'A' and (resid 495 through 506 )A495 - 506
11X-RAY DIFFRACTION11chain 'A' and (resid 507 through 516 )A507 - 516
12X-RAY DIFFRACTION12chain 'A' and (resid 517 through 528 )A517 - 528
13X-RAY DIFFRACTION13chain 'H' and (resid 1 through 17 )H1 - 17
14X-RAY DIFFRACTION14chain 'H' and (resid 18 through 59 )H18 - 59
15X-RAY DIFFRACTION15chain 'H' and (resid 60 through 82 )H60 - 82
16X-RAY DIFFRACTION16chain 'H' and (resid 83 through 113 )H83 - 113
17X-RAY DIFFRACTION17chain 'H' and (resid 114 through 138 )H114 - 138
18X-RAY DIFFRACTION18chain 'H' and (resid 139 through 161 )H139 - 161
19X-RAY DIFFRACTION19chain 'H' and (resid 162 through 192 )H162 - 192
20X-RAY DIFFRACTION20chain 'H' and (resid 193 through 207 )H193 - 207
21X-RAY DIFFRACTION21chain 'H' and (resid 208 through 219 )H208 - 219
22X-RAY DIFFRACTION22chain 'L' and (resid 1 through 18 )L1 - 18
23X-RAY DIFFRACTION23chain 'L' and (resid 19 through 75 )L19 - 75
24X-RAY DIFFRACTION24chain 'L' and (resid 76 through 103 )L76 - 103
25X-RAY DIFFRACTION25chain 'L' and (resid 104 through 114 )L104 - 114
26X-RAY DIFFRACTION26chain 'L' and (resid 115 through 129 )L115 - 129
27X-RAY DIFFRACTION27chain 'L' and (resid 130 through 164 )L130 - 164
28X-RAY DIFFRACTION28chain 'L' and (resid 165 through 214 )L165 - 214

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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