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- PDB-7lm8: Crystal structure of SARS-CoV-2 spike protein receptor-binding do... -

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Entry
Database: PDB / ID: 7lm8
TitleCrystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with two cross-neutralizing antibodies CV38-142 and COVA1-16 Fabs isolated from COVID-19 patients
Components
  • (COVA1-16 Fab ...) x 2
  • (CV38-142 Fab ...) x 2
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / SARS-CoV / Antibody / Spike / Coronavirus / COVID-19 / SARS / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex / Cross-Neutralization / Synergy / 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 / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.936 Å
AuthorsLiu, H. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
Bill & Melinda Gates FoundationINV-004923 United States
Citation
Journal: Cell Host Microbe / Year: 2021
Title: A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection.
Authors: Hejun Liu / Meng Yuan / Deli Huang / Sandhya Bangaru / Fangzhu Zhao / Chang-Chun D Lee / Linghang Peng / Shawn Barman / Xueyong Zhu / David Nemazee / Dennis R Burton / Marit J van Gils / ...Authors: Hejun Liu / Meng Yuan / Deli Huang / Sandhya Bangaru / Fangzhu Zhao / Chang-Chun D Lee / Linghang Peng / Shawn Barman / Xueyong Zhu / David Nemazee / Dennis R Burton / Marit J van Gils / Rogier W Sanders / Hans-Christian Kornau / S Momsen Reincke / Harald Prüss / Jakob Kreye / Nicholas C Wu / Andrew B Ward / Ian A Wilson /
Abstract: Coronaviruses have caused several human epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Prophylactic vaccines and therapeutic antibodies have already shown striking ...Coronaviruses have caused several human epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Prophylactic vaccines and therapeutic antibodies have already shown striking effectiveness against COVID-19. Nevertheless, concerns remain about antigenic drift in SARS-CoV-2 as well as threats from other sarbecoviruses. Cross-neutralizing antibodies to SARS-related viruses provide opportunities to address such concerns. Here, we report on crystal structures of a cross-neutralizing antibody, CV38-142, in complex with the receptor-binding domains from SARS-CoV-2 and SARS-CoV. Recognition of the N343 glycosylation site and water-mediated interactions facilitate cross-reactivity of CV38-142 to SARS-related viruses, allowing the antibody to accommodate antigenic variation in these viruses. CV38-142 synergizes with other cross-neutralizing antibodies, notably COVA1-16, to enhance neutralization of SARS-CoV and SARS-CoV-2, including circulating variants of concern B.1.1.7 and B.1.351. Overall, this study provides valuable information for vaccine and therapeutic design to address current and future antigenic drift in SARS-CoV-2 and to protect against zoonotic SARS-related coronaviruses.
#1: Journal: Biorxiv / Year: 2021
Title: A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection.
Authors: Liu, H. / Yuan, M. / Huang, D. / Bangaru, S. / Lee, C.D. / Peng, L. / Zhu, X. / Nemazee, D. / van Gils, M.J. / Sanders, R.W. / Kornau, H.C. / Reincke, S.M. / Pruss, H. / Kreye, J. / Wu, N.C. ...Authors: Liu, H. / Yuan, M. / Huang, D. / Bangaru, S. / Lee, C.D. / Peng, L. / Zhu, X. / Nemazee, D. / van Gils, M.J. / Sanders, R.W. / Kornau, H.C. / Reincke, S.M. / Pruss, H. / Kreye, J. / Wu, N.C. / Ward, A.B. / Wilson, I.A.
History
DepositionFeb 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: COVA1-16 Fab heavy chain
L: COVA1-16 Fab light chain
M: CV38-142 Fab heavy chain
N: CV38-142 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,23722
Polymers122,5125
Non-polymers1,72617
Water18,1411007
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)59.664, 148.234, 162.257
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 4 types, 4 molecules HLMN

#2: Antibody COVA1-16 Fab heavy chain


Mass: 25100.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody COVA1-16 Fab light chain


Mass: 23502.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#4: Antibody CV38-142 Fab heavy chain


Mass: 24068.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#5: Antibody CV38-142 Fab light chain


Mass: 23745.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Spike protein S1


Mass: 26095.348 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: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 1023 molecules

#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1007 / Source method: isolated from a natural source / Formula: H2O

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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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 10% (w/v) polyethylene glycol 6000, 0.1 M citric acid pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.936→50 Å / Num. obs: 107834 / % possible obs: 100 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.028 / Rrim(I) all: 0.09 / Χ2: 0.962 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.94-1.978.30.87352870.7340.3220.9330.939
1.97-2.019.10.7553290.8180.2630.7960.947
2.01-2.059.90.68153120.8650.2270.7190.965
2.05-2.0910.70.61653380.8910.1970.6481.001
2.09-2.1410.60.52353710.9160.1670.550.967
2.14-2.1810.50.43652720.9430.140.4580.981
2.18-2.2410.10.3853710.9460.1260.40.992
2.24-2.310.50.3353570.9610.1060.3471.018
2.3-2.3710.40.2853280.9720.0910.2951.002
2.37-2.4410.50.24653550.9790.0790.2591.002
2.44-2.5310.70.2153400.9830.0670.2211.013
2.53-2.6310.50.17153800.9890.0550.181.023
2.63-2.7510.10.1454050.9910.0460.1471.031
2.75-2.910.50.1153640.9940.0360.1160.99
2.9-3.0810.50.08853780.9950.0280.0930.995
3.08-3.3210.70.06654520.9970.0210.070.962
3.32-3.6510.30.05253980.9980.0170.0550.941
3.65-4.1810.50.04454830.9980.0140.0460.873
4.18-5.2610.30.03955320.9990.0130.0410.819
5.26-509.90.03857820.9980.0130.040.776

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JMW

7jmw


Resolution: 1.936→33.708 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2007 5355 5.01 %
Rwork0.1687 101477 -
obs0.1703 106832 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.66 Å2 / Biso mean: 22.8828 Å2 / Biso min: 8.55 Å2
Refinement stepCycle: final / Resolution: 1.936→33.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8192 0 113 1007 9312
Biso mean--32.97 31.62 -
Num. residues----1071
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9364-1.95840.30131450.2377272282
1.9584-1.98140.2651610.2128320693
1.9814-2.00560.26311740.2005327297
2.0056-2.0310.23791700.1993334299
2.031-2.05770.27291750.1965341999
2.0577-2.08590.19991750.18873306100
2.0859-2.11570.24841720.1883413100
2.1157-2.14720.22251900.17693347100
2.1472-2.18080.23611820.17453367100
2.1808-2.21650.18731810.17383424100
2.2165-2.25470.23231810.16563350100
2.2547-2.29570.1981670.16733416100
2.2957-2.33990.19211620.16583372100
2.3399-2.38760.21081770.1733440100
2.3876-2.43950.22671550.17413384100
2.4395-2.49630.22791700.17573424100
2.4963-2.55870.2021860.17153365100
2.5587-2.62780.22732020.17713378100
2.6278-2.70510.20191920.17673429100
2.7051-2.79240.21381800.17653367100
2.7924-2.89210.2281610.17563443100
2.8921-3.00790.18511690.17823439100
3.0079-3.14470.20091720.17343461100
3.1447-3.31030.20192030.16623390100
3.3103-3.51750.19061640.16313457100
3.5175-3.78880.17712000.15133424100
3.7888-4.16940.16691740.14593470100
4.1694-4.77130.15471840.1253492100
4.7713-6.00580.15492140.1523506100
6.0058-33.7080.21842170.19293652100
Refinement TLS params.Method: refined / Origin x: -12.5851 Å / Origin y: -33.5397 Å / Origin z: 19.4384 Å
111213212223313233
T0.0979 Å2-0.009 Å20.0067 Å2-0.1429 Å20.0006 Å2--0.0757 Å2
L0.1527 °2-0.2446 °2-0.004 °2-0.7203 °2-0.0337 °2--0.0708 °2
S-0.0106 Å °-0.0255 Å °0.0049 Å °0.0478 Å °0.0102 Å °0.0162 Å °0.0102 Å °-0.0042 Å °-0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA334 - 529
2X-RAY DIFFRACTION1allA629 - 632
3X-RAY DIFFRACTION1allH1 - 215
4X-RAY DIFFRACTION1allL1 - 213
5X-RAY DIFFRACTION1allM1 - 214
6X-RAY DIFFRACTION1allN1 - 215
7X-RAY DIFFRACTION1allS1 - 16
8X-RAY DIFFRACTION1allW1 - 1007

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