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- PDB-6xkp: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6xkp
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-270
Components
  • CV07-270 Heavy Chain
  • CV07-270 Light Chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Antibody / Spike / Coronavirus / COVID-19 / IMMUNE SYSTEM / 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 / 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsLiu, H. / Yuan, M. / Zhu, X. / Wu, N.C. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI139445 United States
CitationJournal: Cell / Year: 2020
Title: A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model.
Authors: Kreye, J. / Reincke, S.M. / Kornau, H.C. / Sanchez-Sendin, E. / Corman, V.M. / Liu, H. / Yuan, M. / Wu, N.C. / Zhu, X. / Lee, C.D. / Trimpert, J. / Holtje, M. / Dietert, K. / Stoffler, L. / ...Authors: Kreye, J. / Reincke, S.M. / Kornau, H.C. / Sanchez-Sendin, E. / Corman, V.M. / Liu, H. / Yuan, M. / Wu, N.C. / Zhu, X. / Lee, C.D. / Trimpert, J. / Holtje, M. / Dietert, K. / Stoffler, L. / von Wardenburg, N. / van Hoof, S. / Homeyer, M.A. / Hoffmann, J. / Abdelgawad, A. / Gruber, A.D. / Bertzbach, L.D. / Vladimirova, D. / Li, L.Y. / Barthel, P.C. / Skriner, K. / Hocke, A.C. / Hippenstiel, S. / Witzenrath, M. / Suttorp, N. / Kurth, F. / Franke, C. / Endres, M. / Schmitz, D. / Jeworowski, L.M. / Richter, A. / Schmidt, M.L. / Schwarz, T. / Muller, M.A. / Drosten, C. / Wendisch, D. / Sander, L.E. / Osterrieder, N. / Wilson, I.A. / Pruss, H.
History
DepositionJun 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: 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_PubMed / _citation.title
Revision 1.2Nov 25, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 9, 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

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Assembly

Deposited unit
A: Spike protein S1
B: Spike protein S1
H: CV07-270 Heavy Chain
L: CV07-270 Light Chain
M: CV07-270 Heavy Chain
N: CV07-270 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,46116
Polymers147,2506
Non-polymers1,21110
Water00
1
A: Spike protein S1
H: CV07-270 Heavy Chain
L: CV07-270 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3279
Polymers73,6253
Non-polymers7026
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-84 kcal/mol
Surface area27240 Å2
MethodPISA
2
B: Spike protein S1
M: CV07-270 Heavy Chain
N: CV07-270 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1357
Polymers73,6253
Non-polymers5094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-66 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.020, 151.785, 66.015
Angle α, β, γ (deg.)90.000, 95.440, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12H
22M
13L
23N

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPROPROAA334 - 52716 - 209
21ASNASNPROPROBB334 - 52716 - 209
12GLNGLNLYSLYSHC1 - 2141 - 230
22GLNGLNLYSLYSME1 - 2141 - 230
13ALAALATHRTHRLD3 - 2103 - 213
23ALAALATHRTHRNF3 - 2103 - 213

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Spike protein S1


Mass: 26095.348 Da / Num. of mol.: 2
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
#2: Antibody CV07-270 Heavy Chain


Mass: 24817.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody CV07-270 Light Chain


Mass: 22711.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
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: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.5 0.2 M sodium chloride 2 M ammonium sulfate 15% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 41624 / % possible obs: 90.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.099 / Rrim(I) all: 0.222 / Χ2: 0.7 / Net I/σ(I): 3.7 / Num. measured all: 195146
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.60.89320890.6760.5051.0310.39790.8
2.75-2.83.90.87421130.7210.4720.9970.40292.6
2.8-2.854.20.76121310.8010.3990.8630.40992.7
2.85-2.914.40.7720690.7880.3980.870.41192.3
2.91-2.974.60.6921320.7820.350.7760.43392.2
2.97-3.044.70.60620530.8230.3040.680.45991
3.04-3.124.70.47720400.8920.2390.5360.45888.4
3.12-3.24.70.39518740.9140.1980.4430.51282.2
3.2-3.34.80.3219310.9430.1580.3580.53684.3
3.3-3.44.90.28421880.960.1390.3170.55696.1
3.4-3.5250.2521710.9640.1210.2780.58495
3.52-3.6650.20721860.9750.1010.230.65994.8
3.66-3.834.90.17321490.980.0850.1930.72393.8
3.83-4.034.90.14921080.9810.0730.1660.85392.9
4.03-4.294.90.12220820.990.060.1370.9690.8
4.29-4.624.80.10519630.9910.0510.1171.10785.3
4.62-5.084.90.10219120.9920.0490.1131.07783.4
5.08-5.815.10.10122170.9920.0480.1120.89295.9
5.81-7.3250.09821480.9910.0470.1090.87793.3
7.32-504.90.06120680.9960.0290.0681.39688.2

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41

6w41


Resolution: 2.72→49.73 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.866 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.195 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2694 2055 4.9 %RANDOM
Rwork0.2199 ---
obs0.2223 39568 89.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.71 Å2 / Biso mean: 37.534 Å2 / Biso min: 8.26 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å20 Å2-0.64 Å2
2---0.4 Å20 Å2
3----2.61 Å2
Refinement stepCycle: final / Resolution: 2.72→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9177 0 68 0 9245
Biso mean--67.74 --
Num. residues----1253
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A52220.16
12B52220.16
21H61150.14
22M61150.14
31L52330.16
32N52330.16
LS refinement shellResolution: 2.72→2.786 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.391 137 -
Rwork0.32 2581 -
obs--79.66 %

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