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- PDB-7u8e: Crystal structure of antibody Ab246 in complex with SARS-CoV-2 re... -

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Basic information

Entry
Database: PDB / ID: 7u8e
TitleCrystal structure of antibody Ab246 in complex with SARS-CoV-2 receptor binding domain
Components
  • (Antibody Ab246 Fab ...) x 2
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Neutralizing antibody / SARS-CoV-2 / Ab246 / receptor binding domain / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN
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 / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsSankhala, R.S. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-18-2-0040 United States
CitationJournal: Structure / Year: 2024
Title: Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain.
Authors: Sankhala, R.S. / Dussupt, V. / Chen, W.H. / Bai, H. / Martinez, E.J. / Jensen, J.L. / Rees, P.A. / Hajduczki, A. / Chang, W.C. / Choe, M. / Yan, L. / Sterling, S.L. / Swafford, I. / Kuklis, ...Authors: Sankhala, R.S. / Dussupt, V. / Chen, W.H. / Bai, H. / Martinez, E.J. / Jensen, J.L. / Rees, P.A. / Hajduczki, A. / Chang, W.C. / Choe, M. / Yan, L. / Sterling, S.L. / Swafford, I. / Kuklis, C. / Soman, S. / King, J. / Corbitt, C. / Zemil, M. / Peterson, C.E. / Mendez-Rivera, L. / Townsley, S.M. / Donofrio, G.C. / Lal, K.G. / Tran, U. / Green, E.C. / Smith, C. / de Val, N. / Laing, E.D. / Broder, C.C. / Currier, J.R. / Gromowski, G.D. / Wieczorek, L. / Rolland, M. / Paquin-Proulx, D. / van Dyk, D. / Britton, Z. / Rajan, S. / Loo, Y.M. / McTamney, P.M. / Esser, M.T. / Polonis, V.R. / Michael, N.L. / Krebs, S.J. / Modjarrad, K. / Joyce, M.G.
History
DepositionMar 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 10, 2024Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: Antibody Ab246 Fab heavy chain
L: Antibody Ab246 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,66311
Polymers70,8543
Non-polymers8098
Water3,603200
1
H: Antibody Ab246 Fab heavy chain
L: Antibody Ab246 Fab light chain
hetero molecules

A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,66311
Polymers70,8543
Non-polymers8098
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area5610 Å2
ΔGint-30 kcal/mol
Surface area30490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.797, 41.603, 98.991
Angle α, β, γ (deg.)90.000, 107.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody Antibody Ab246 Fab heavy chain


Mass: 24152.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fragment antigen-binding (Fab) heavy chain / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Antibody Ab246 Fab light chain


Mass: 23628.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fragment antigen-binding (Fab) light chain / 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: 23073.766 Da / Num. of mol.: 1 / Fragment: receptor binding domain (RBD)
Source method: isolated from a genetically manipulated source
Details: Viral protein
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#4: 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
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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Non-polymers , 3 types, 207 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 33571 / % possible obs: 96.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 26.02 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.08 / Rrim(I) all: 0.148 / Rsym value: 0.124 / Χ2: 0.92 / Net I/av σ(I): 9.78 / Net I/σ(I): 9.78
Reflection shellResolution: 2.29→2.38 Å / Num. unique obs: 3156 / CC1/2: 0.897 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H0E

6h0e


Resolution: 2.29→19.899 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1433 5 %
Rwork0.204 27223 -
obs0.2062 28656 82.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.62 Å2 / Biso mean: 44.9468 Å2 / Biso min: 11.18 Å2
Refinement stepCycle: final / Resolution: 2.29→19.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4841 0 51 200 5092
Biso mean--52.07 38.67 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045031
X-RAY DIFFRACTIONf_angle_d0.6776852
X-RAY DIFFRACTIONf_chiral_restr0.044754
X-RAY DIFFRACTIONf_plane_restr0.004871
X-RAY DIFFRACTIONf_dihedral_angle_d13.932983
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.29-2.37160.3366910.2457171652
2.3716-2.46640.28381040.2392198061
2.4664-2.57840.31561190.2388225769
2.5784-2.7140.31381280.2398244875
2.714-2.88360.26521470.239277884
2.8836-3.10550.30531630.2294310694
3.1055-3.41660.25181700.2111323898
3.4166-3.90770.2331670.1891318096
3.9077-4.9110.18091720.1638326298
4.911-19.8990.24091720.1959325895
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)
12.70960.0007-0.69892.39851.28080.86120.09530.2350.0199-0.71520.0092-0.7048-0.40660.8144-0.17180.38310.09050.19810.89870.11220.5102-9.572514.602821.2964
22.8215-1.5163-2.6642.75622.67483.36110.24950.52340.2998-0.86060.2142-0.4542-0.55570.7393-0.44110.73710.08420.36470.78770.16590.6578-14.026416.486612.954
31.9699-1.04611.99025.2783-4.49844.51840.22760.9169-0.8238-0.9929-0.1102-0.70621.4531.2077-0.06760.53550.30650.17061.01960.05590.7285-11.54110.658716.2828
46.4873-0.02931.88718.7212-2.20028.7821-0.13940.7722-0.6298-1.02810.136-0.75950.87950.80430.01830.37920.12880.09080.5364-0.04440.4347-21.86064.172512.7203
54.5529-0.3775-0.96791.6886-0.43642.37140.1267-0.0984-0.0036-0.030.0746-0.0011-0.0775-0.20980.08660.05930.14460.10550.80910.08320.4573-18.131910.2128.2807
61.4883-0.3709-0.00430.518-0.09810.0378-0.0341-0.64010.3307-0.01130.0065-0.2319-0.16680.14230.02970.17630.23820.04741.1309-0.05330.3015-20.303315.057234.6341
72.40472.0762-1.60182.9193-0.39751.9281-0.2886-1.1020.9080.52910.11180.3266-0.3257-0.28760.07370.35720.0618-0.02721.4107-0.29930.6729-20.555223.30249.7947
83.9872-0.2154-0.34951.23860.7362.910.0173-0.7103-0.11570.10970.1246-0.1703-0.1146-0.1716-0.01230.21210.11770.04030.92510.15730.4003-12.62116.918632.3115
93.8402-0.5603-3.0284.69770.57855.36740.47261.33880.0868-2.2668-0.2320.6835-0.6187-0.7567-0.21581.3550.08410.02321.3680.1640.523-22.148513.32834.1376
102.1789-1.0464-0.04052.7059-0.79781.351-0.1338-0.0840.0287-0.0817-0.2018-0.1602-0.00160.21520.12270.3060.09940.0322-0.09250.09720.2201-49.35845.438811.3482
112.44810.786-0.26550.67580.60771.481-0.07310.0313-0.146-0.07040.0984-0.06350.15890.228-0.0710.24330.05640.04870.05140.0440.1816-45.44864.051710.5512
121.765-1.4567-0.2412.11580.09220.97150.0119-0.08280.37820.0132-0.13110.1009-0.34850.13620.06160.3518-0.01310.00770.1102-0.01740.2932-67.332523.668618.8345
131.35590.09510.22250.1798-0.13211.2097-0.1159-0.9895-0.36030.3373-0.0154-0.09480.47820.3035-0.0230.31720.29-0.07590.61780.23380.0689-45.24750.496232.6259
141.9556-0.76960.95681.3905-0.28270.4922-0.016-0.7260.26640.0294-0.05610.02540.09750.24840.0670.21090.08480.00830.659-0.0360.1871-74.745921.224632.7957
151.9635-1.41591.14124.41420.06023.93540.1694-0.5921-0.22380.1905-0.29840.26680.0936-0.00810.08820.2189-0.02720.01220.5449-0.01120.2135-80.963720.912733.2167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 333 through 353 )A333 - 353
2X-RAY DIFFRACTION2chain 'A' and (resid 354 through 364 )A354 - 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 479 )A410 - 479
7X-RAY DIFFRACTION7chain 'A' and (resid 480 through 494 )A480 - 494
8X-RAY DIFFRACTION8chain 'A' and (resid 495 through 516 )A495 - 516
9X-RAY DIFFRACTION9chain 'A' and (resid 517 through 530 )A517 - 530
10X-RAY DIFFRACTION10chain 'H' and (resid 1 through 66 )H1 - 66
11X-RAY DIFFRACTION11chain 'H' and (resid 67 through 100F)H67 - 100
12X-RAY DIFFRACTION12chain 'H' and (resid 100G through 213 )H100
13X-RAY DIFFRACTION13chain 'L' and (resid 2 through 104 )L2 - 104
14X-RAY DIFFRACTION14chain 'L' and (resid 105 through 153 )L105 - 153
15X-RAY DIFFRACTION15chain 'L' and (resid 154 through 211 )L154 - 211

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