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- PDB-7k9z: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7k9z
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with the Fab fragments of neutralizing antibodies 298 and 52
Components
  • 298 Fab Heavy Chain
  • 298 Fab Light Chain
  • 52 Fab Heavy Chain
  • 52 Fab Light Chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / Receptor Binding Domain / Neutralizing antibodies
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 / 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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: 2.95 Å
AuthorsNewton, J.C. / Kucharska, I. / Rujas, E. / Cui, H. / Julien, J.P.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)6280100058 Canada
Canadian Institutes of Health Research (CIHR)PJ4-169662 Canada
Citation
Journal: Nat Commun / Year: 2021
Title: Multivalency transforms SARS-CoV-2 antibodies into ultrapotent neutralizers.
Authors: Edurne Rujas / Iga Kucharska / Yong Zi Tan / Samir Benlekbir / Hong Cui / Tiantian Zhao / Gregory A Wasney / Patrick Budylowski / Furkan Guvenc / Jocelyn C Newton / Taylor Sicard / Anthony ...Authors: Edurne Rujas / Iga Kucharska / Yong Zi Tan / Samir Benlekbir / Hong Cui / Tiantian Zhao / Gregory A Wasney / Patrick Budylowski / Furkan Guvenc / Jocelyn C Newton / Taylor Sicard / Anthony Semesi / Krithika Muthuraman / Amy Nouanesengsy / Clare Burn Aschner / Katherine Prieto / Stephanie A Bueler / Sawsan Youssef / Sindy Liao-Chan / Jacob Glanville / Natasha Christie-Holmes / Samira Mubareka / Scott D Gray-Owen / John L Rubinstein / Bebhinn Treanor / Jean-Philippe Julien /
Abstract: SARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a ...SARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a modular subunit to drive oligomerization of antibody fragments and transform antibodies targeting SARS-CoV-2 into exceptionally potent neutralizers. Using this platform, half-maximal inhibitory concentration (IC) values as low as 9 × 10 M are achieved as a result of up to 10,000-fold potency enhancements compared to corresponding IgGs. Combination of three different antibody specificities and the fragment crystallizable (Fc) domain on a single multivalent molecule conferred the ability to overcome viral sequence variability together with outstanding potency and IgG-like bioavailability. The MULTi-specific, multi-Affinity antiBODY (Multabody or MB) platform thus uniquely leverages binding avidity together with multi-specificity to deliver ultrapotent and broad neutralizers against SARS-CoV-2. The modularity of the platform also makes it relevant for rapid evaluation against other infectious diseases of global health importance. Neutralizing antibodies are a promising therapeutic for SARS-CoV-2.
#1: Journal: Biorxiv / Year: 2020
Title: Multivalency transforms SARS-CoV-2 antibodies into broad and ultrapotent neutralizers
Authors: Rujas, E. / Kucharska, I. / Tan, Y.Z. / Benlekbir, S. / Cui, H. / Zhao, T. / Wasney, G. / Budylowski, P. / Guvenc, F. / Newton, J.C. / Sicard, T. / Semesi, A. / Muthuraman, K. / ...Authors: Rujas, E. / Kucharska, I. / Tan, Y.Z. / Benlekbir, S. / Cui, H. / Zhao, T. / Wasney, G. / Budylowski, P. / Guvenc, F. / Newton, J.C. / Sicard, T. / Semesi, A. / Muthuraman, K. / Nouanesengsy, A. / Prieto, K. / Bueler, S.A. / Youssef, S. / Liao-Chan, S. / Glanville, J. / Christie-Holmes, N. / Mubareka, S. / Gray-Owen, S.D. / Rubinstein, J.L. / Treanor, B. / Julien, J.P.
History
DepositionSep 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name
Revision 1.2Jul 28, 2021Group: Database references / Category: citation / citation_author
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / software
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 52 Fab Heavy Chain
L: 52 Fab Light Chain
A: 298 Fab Light Chain
B: 298 Fab Heavy Chain
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,0136
Polymers119,7925
Non-polymers2211
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-59 kcal/mol
Surface area47550 Å2
Unit cell
Length a, b, c (Å)87.617, 87.617, 325.096
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Antibody , 4 types, 4 molecules HLAB

#1: Antibody 52 Fab Heavy Chain


Mass: 23277.129 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 52 Fab Light Chain


Mass: 23227.709 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 298 Fab Light Chain


Mass: 24227.836 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: Antibody 298 Fab Heavy Chain


Mass: 23245.969 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 E

#5: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein / Spike glycoprotein


Mass: 25813.070 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
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) 2-propanol, 20% (w/v) PEG 4000, 0.1 M sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.95→39.66 Å / Num. obs: 31545 / % possible obs: 99.9 % / Redundancy: 15.7 % / Biso Wilson estimate: 78.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.043 / Net I/σ(I): 12.3
Reflection shellResolution: 2.95→3.05 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3060 / CC1/2: 0.863 / Rpim(I) all: 0.201 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XPREP2015/1data reduction
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
XDS0.94data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DN3, 5CZX, 6XDG

4dn3

5czx

6xdg


Resolution: 2.95→39.61 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2871 1602 5.1 %
Rwork0.2612 29820 -
obs0.2625 31422 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.78 Å2 / Biso mean: 103.9794 Å2 / Biso min: 70.55 Å2
Refinement stepCycle: final / Resolution: 2.95→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8047 0 14 0 8061
Biso mean--113.13 --
Num. residues----1057
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.040.46171730.41492594276798
3.04-3.150.35051330.37472632276598
3.15-3.280.35211360.36282638277499
3.28-3.430.35791130.33882673278699
3.43-3.610.35761310.32662683281499
3.61-3.830.36321650.30592687285299
3.83-4.130.2881280.277327112839100
4.13-4.540.30541870.235426982885100
4.54-5.20.23991430.210327522895100
5.2-6.540.27391420.233727882930100
6.54-39.610.21051510.21429643115100
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)
11.1157-0.9879-0.87547.17153.46983.1083-0.2859-0.05380.3357-0.35210.4456-0.2342-0.60770.125-0.16580.9105-0.2353-0.04251.84-0.17730.6253-9.1066-17.990956.7941
21.43580.82881.18972.90321.41212.0438-0.13580.00630.30610.4520.05950.133-0.664-0.41510.03741.1359-0.0182-0.03751.6808-0.07940.5269-16.8922-16.413560.075
31.7497-0.12820.1557.2407-1.1055.6143-0.3716-0.37020.28610.39790.1995-0.3454-1.763-0.0750.15761.3365-0.0898-0.25791.7504-0.23430.7611-4.0835-14.661491.2993
40.261-0.6179-0.34321.83150.86940.7793-0.3027-0.28210.1403-0.41840.5144-0.3884-0.3777-0.038-0.31391.9401-0.6224-0.29561.98120.12951.01324.7442-11.520592.4936
53.2173-0.39552.17781.8835-1.46982.9283-0.0348-0.433-0.02830.41410.12060.39720.2802-0.8507-0.01640.89830.04190.07951.9648-0.10960.4463-26.9571-34.259870.5023
60.35660.0667-0.08551.35250.56481.6887-0.0751-0.2442-0.15640.3253-0.36390.0268-0.4236-0.48540.15770.766-0.06120.08162.42-0.321-0.2496-19.8671-35.477471.6878
72.7177-0.0140.04993.58860.10372.197-0.2636-0.3740.31330.3687-0.03630.1317-1.3174-1.31860.29471.45310.346-0.27992.0211-0.14740.6914-13.9663-14.071997.0331
85.05181.16120.72680.33260.5494.2483-0.0295-0.15580.76520.2966-0.72810.8958-1.3681-1.77310.74141.64450.3884-0.08252.145-0.33180.7879-17.9666-15.439998.0823
94.12420.8855-0.00323.61680.6174.35070.0317-0.45450.05830.0932-0.45110.45060.3554-0.35440.44090.98170.0343-0.02831.3912-0.15170.433-21.3121-48.916618.4523
100.203-0.403-0.27210.73550.91982.08210.0041-0.1248-0.0672-0.2386-0.1565-0.1417-0.1179-0.02590.19031.0290.06810.0821.2441-0.03650.4294-1.9984-47.65890.7251
116.81210.07971.05152.12520.65680.47610.31310.2198-0.1857-0.2257-0.103-0.4019-0.5708-0.0991-0.24711.21270.3220.11581.26190.01740.50476.1672-53.1717-7.9075
121.21971.0121.16522.8244-1.08023.22940.1268-0.11390.35150.0433-0.49320.0345-0.88330.05080.361.04420.02590.00031.7495-0.11550.5088-6.4661-30.498623.9246
133.5991.2838-3.36992.2730.34095.51-0.054-0.6420.1484-0.1424-0.2550.1015-0.38840.75390.30710.9545-0.044-0.131.7675-0.06020.4795-4.3782-34.651925.7139
144.21770.06891.7822.0327-0.27652.6295-0.0038-0.19010.2276-0.76430.1383-0.2925-1.19170.1195-0.15851.45030.10450.05591.368-0.11530.53323.551-35.6039-7.6371
157.234-1.4571-1.13534.5937-0.5481.6651-0.2612-1.44870.79020.34690.41950.2533-1.07470.5754-0.21741.18830.09950.051.7064-0.16010.6145-41.7227-14.874651.7127
164.1551-1.2292-2.07112.08020.02057.3294-0.7146-1.29030.12990.7914-0.08410.1466-0.55050.55560.56050.84970.11970.05511.7417-0.09770.6213-46.2223-19.736456.8371
173.4953-0.4362-2.80550.35920.01157.6835-0.3245-0.53160.35260.3385-0.02190.4892-0.8427-0.75540.38750.90280.24640.03971.2482-0.05690.7418-53.953-14.396843.1879
181.46410.33041.00232.4202-1.699.5985-0.1671-0.62350.33130.23350.35750.44310.0068-1.265-0.1290.72480.1640.0622.1815-0.12750.5423-57.4894-23.54548.6948
192.53381.04590.45155.5564-0.9330.36490.241-0.00780.0718-0.3642-0.08590.0727-0.4225-0.1659-0.23870.8630.0710.00391.5993-0.11190.3892-41.9369-26.345942.5731
201.103-0.4271-0.10580.26610.59183.27730.15580.27790.4795-0.41220.2532-0.2133-1.19240.4974-0.08140.9091-0.0298-0.13952.4517-0.11660.2124-27.9806-24.119540.0531
211.6028-0.5842-0.64850.35480.57011.2285-0.2136-0.0729-0.13260.1840.0930.44580.47040.51940.06540.76130.18220.04252.1457-0.1226-0.0529-27.9514-37.213746.9098
221.34930.1084-1.09881.64982.14163.89180.011-0.1213-0.1879-0.4385-0.1852-0.05480.13440.6940.10570.84790.07210.03832.0979-0.16360.3544-17.9778-34.805540.9053
233.66260.2074-1.48981.83970.81961.07610.0684-0.03180.6072-0.5379-0.051-0.6402-0.1680.5246-0.07960.9773-0.0547-0.02732.0052-0.07730.4114-38.5722-19.661238.357
240.32850.64570.09352.0362-1.67724.6082-0.1747-0.9059-0.31120.68160.56020.3702-1.3952-0.8631-0.33441.04460.08290.21372.11920.03020.6172-56.073-24.393262.1991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 32 )H1 - 32
2X-RAY DIFFRACTION2chain 'H' and (resid 33 through 119 )H33 - 119
3X-RAY DIFFRACTION3chain 'H' and (resid 120 through 188 )H120 - 188
4X-RAY DIFFRACTION4chain 'H' and (resid 189 through 213 )H189 - 213
5X-RAY DIFFRACTION5chain 'L' and (resid 0 through 38 )L0 - 38
6X-RAY DIFFRACTION6chain 'L' and (resid 39 through 115 )L39 - 115
7X-RAY DIFFRACTION7chain 'L' and (resid 116 through 150 )L116 - 150
8X-RAY DIFFRACTION8chain 'L' and (resid 151 through 211 )L151 - 211
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 90 )A1 - 90
10X-RAY DIFFRACTION10chain 'A' and (resid 91 through 139 )A91 - 139
11X-RAY DIFFRACTION11chain 'A' and (resid 140 through 214 )A140 - 214
12X-RAY DIFFRACTION12chain 'B' and (resid 2 through 40 )B2 - 40
13X-RAY DIFFRACTION13chain 'B' and (resid 41 through 119 )B41 - 119
14X-RAY DIFFRACTION14chain 'B' and (resid 120 through 216 )B120 - 216
15X-RAY DIFFRACTION15chain 'E' and (resid 333 through 352 )E333 - 352
16X-RAY DIFFRACTION16chain 'E' and (resid 353 through 364 )E353 - 364
17X-RAY DIFFRACTION17chain 'E' and (resid 365 through 375 )E365 - 375
18X-RAY DIFFRACTION18chain 'E' and (resid 376 through 393 )E376 - 393
19X-RAY DIFFRACTION19chain 'E' and (resid 394 through 442 )E394 - 442
20X-RAY DIFFRACTION20chain 'E' and (resid 443 through 459 )E443 - 459
21X-RAY DIFFRACTION21chain 'E' and (resid 460 through 479 )E460 - 479
22X-RAY DIFFRACTION22chain 'E' and (resid 480 through 494 )E480 - 494
23X-RAY DIFFRACTION23chain 'E' and (resid 495 through 516 )E495 - 516
24X-RAY DIFFRACTION24chain 'E' and (resid 517 through 527 )E517 - 527

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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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