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

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Basic information

Entry
Database: PDB / ID: 6xkq
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-250
Components
  • CV07-250 Heavy Chain
  • CV07-250 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 / 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: 2.55 Å
AuthorsYuan, M. / Liu, H. / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: CV07-250 Heavy Chain
L: CV07-250 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3675
Polymers72,9243
Non-polymers4422
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-23 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.970, 80.070, 153.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Antibody CV07-250 Heavy Chain


Mass: 23966.656 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 CV07-250 Light Chain


Mass: 22862.197 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: 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.: 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.085 M HEPES pH 7.5 10% (v/v) ethylene glycol 15% (v/v) glycerol 8.5% (v/v) 2-propanol 17% (w/v) polyethylene glycol 4000

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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: 2.55→50 Å / Num. obs: 27942 / % possible obs: 99.6 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.041 / Rrim(I) all: 0.126 / Χ2: 0.969 / Net I/σ(I): 6.2 / Num. measured all: 245129
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.596.50.94613520.710.3891.0270.40498.9
2.59-2.647.20.81813630.7970.320.8810.40799.9
2.64-2.6980.70113720.8530.260.750.42599.4
2.69-2.758.40.65913750.8760.2390.7030.41899.6
2.75-2.818.50.56413700.9010.2030.6010.44399.8
2.81-2.877.60.45513650.9320.1720.4880.4698.6
2.87-2.948.70.38713800.9490.1360.4110.49299.8
2.94-3.029.90.34813610.9710.1150.3670.51699.9
3.02-3.119.90.28514100.9760.0940.3010.553100
3.11-3.219.90.23313970.9850.0770.2460.593100
3.21-3.339.70.19213810.9870.0640.2030.674100
3.33-3.469.50.1613950.9920.0540.1690.79899.9
3.46-3.629.30.13614000.9940.0460.1440.89299.8
3.62-3.819.10.11313940.9950.0390.121.095100
3.81-4.058.60.09414040.9950.0330.11.34599.3
4.05-4.367.80.07413760.9970.0270.0791.75698.4
4.36-4.89.90.06914240.9980.0230.0731.79599.9
4.8-5.499.70.06914290.9980.0230.0731.739100
5.49-6.929.20.07114570.9970.0240.0751.699100
6.92-5080.05315370.9980.0190.0562.3899.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41

6w41


Resolution: 2.55→49.102 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 1364 4.89 %
Rwork0.204 26520 -
obs0.2065 27884 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.31 Å2 / Biso mean: 52.2014 Å2 / Biso min: 28.28 Å2
Refinement stepCycle: final / Resolution: 2.55→49.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4420 0 28 77 4525
Biso mean--99.77 49.02 -
Num. residues----583
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5501-2.64120.33351140.2608254297
2.6412-2.74690.25841450.22822594100
2.7469-2.87190.3061210.2177261799
2.8719-3.02330.2751490.20252610100
3.0233-3.21270.24871420.20152667100
3.2127-3.46070.26151290.18962635100
3.4607-3.80890.23121250.19552684100
3.8089-4.35970.26371530.1902262599
4.3597-5.49160.2171450.18762709100
5.4916-49.1020.27291410.2306283799
Refinement TLS params.Method: refined / Origin x: -26.0005 Å / Origin y: -32.7479 Å / Origin z: -26.7316 Å
111213212223313233
T0.3786 Å2-0.0274 Å20.0099 Å2-0.3848 Å2-0.0264 Å2--0.369 Å2
L0.3922 °20.0841 °20.5682 °2-0.6965 °20.4249 °2--1.0629 °2
S-0.0024 Å °0.0635 Å °0.0014 Å °-0.2311 Å °0.0701 Å °0.0574 Å °-0.0177 Å °0.1029 Å °-0.076 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA338 - 528
2X-RAY DIFFRACTION1allH1 - 213
3X-RAY DIFFRACTION1allH214
4X-RAY DIFFRACTION1allL3 - 210
5X-RAY DIFFRACTION1allS1 - 79

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