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- PDB-7bnv: Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Co... -

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Basic information

Entry
Database: PDB / ID: 7bnv
TitleCrystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-300
Components
  • Heavy Chain
  • Light Chain
  • Surface glycoprotein
KeywordsVIRAL PROTEIN / Antibody Immune System
Function / homology
Function and homology information


: / membrane => GO:0016020 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion 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 S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHall, G. / Cowan, R. / Carr, M.
CitationJournal: Front Immunol / Year: 2021
Title: Cross-Reactive SARS-CoV-2 Neutralizing Antibodies From Deep Mining of Early Patient Responses.
Authors: Bullen, G. / Galson, J.D. / Hall, G. / Villar, P. / Moreels, L. / Ledsgaard, L. / Mattiuzzo, G. / Bentley, E.M. / Masters, E.W. / Tang, D. / Millett, S. / Tongue, D. / Brown, R. / ...Authors: Bullen, G. / Galson, J.D. / Hall, G. / Villar, P. / Moreels, L. / Ledsgaard, L. / Mattiuzzo, G. / Bentley, E.M. / Masters, E.W. / Tang, D. / Millett, S. / Tongue, D. / Brown, R. / Diamantopoulos, I. / Parthiban, K. / Tebbutt, C. / Leah, R. / Chaitanya, K. / Ergueta-Carballo, S. / Pazeraitis, D. / Surade, S.B. / Ashiru, O. / Crippa, L. / Cowan, R. / Bowler, M.W. / Campbell, J.I. / Lee, W.J. / Carr, M.D. / Matthews, D. / Pfeffer, P. / Hufton, S.E. / Sawmynaden, K. / Osbourn, J. / McCafferty, J. / Karatt-Vellatt, A.
History
DepositionJan 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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: Surface glycoprotein
H: Heavy Chain
L: Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9514
Polymers74,7303
Non-polymers2211
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-31 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.861, 74.861, 143.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Surface glycoprotein


Mass: 26308.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Homo sapiens (human) / References: UniProt: A0A6M5UN06
#2: Antibody Heavy Chain


Mass: 24528.439 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 Light Chain


Mass: 23892.508 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: 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.: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 16% PEG3350 0.3 M potassium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.35→40.23 Å / Num. obs: 32467 / % possible obs: 99.08 % / Redundancy: 1.9 % / Biso Wilson estimate: 56.48 Å2 / CC1/2: 0.997 / Net I/σ(I): 16.34
Reflection shellResolution: 2.35→2.434 Å / Num. unique obs: 3234 / CC1/2: 0.48

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Processing

Software
NameVersionClassification
REFMACv1refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J

6m0j


Resolution: 2.35→40.23 Å / SU ML: 0.3534 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.5911
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2646 3293 10.15 %
Rwork0.2236 29153 -
obs0.2276 32446 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4799 0 14 165 4978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00394942
X-RAY DIFFRACTIONf_angle_d0.81916742
X-RAY DIFFRACTIONf_chiral_restr0.055741
X-RAY DIFFRACTIONf_plane_restr0.0067870
X-RAY DIFFRACTIONf_dihedral_angle_d13.0348693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.35751300.32251222X-RAY DIFFRACTION99.93
2.38-2.420.36971430.32591231X-RAY DIFFRACTION100
2.42-2.460.35931320.30591201X-RAY DIFFRACTION100
2.46-2.50.3381410.29741244X-RAY DIFFRACTION99.86
2.5-2.540.3211570.30941169X-RAY DIFFRACTION99.92
2.54-2.590.30131660.28881223X-RAY DIFFRACTION99.86
2.59-2.640.33281200.27251227X-RAY DIFFRACTION99.93
2.64-2.690.29231670.27481197X-RAY DIFFRACTION99.71
2.69-2.750.33411580.28311189X-RAY DIFFRACTION99.48
2.75-2.810.31021450.26631184X-RAY DIFFRACTION99.4
2.81-2.880.31911420.28671264X-RAY DIFFRACTION99.58
2.88-2.960.34741230.26191207X-RAY DIFFRACTION99.55
2.96-3.050.30151530.25971194X-RAY DIFFRACTION99.7
3.05-3.150.33691330.25981242X-RAY DIFFRACTION99.78
3.15-3.260.28871080.26851228X-RAY DIFFRACTION99.18
3.26-3.390.29761310.23441216X-RAY DIFFRACTION97.68
3.39-3.540.2741260.23991216X-RAY DIFFRACTION98.82
3.54-3.730.22861380.21641222X-RAY DIFFRACTION99.27
3.73-3.960.2561320.20141224X-RAY DIFFRACTION99.49
3.96-4.270.22111280.19591208X-RAY DIFFRACTION99.48
4.27-4.70.2051330.17351256X-RAY DIFFRACTION99.29
4.7-5.370.21991460.18621212X-RAY DIFFRACTION98.84
5.38-6.770.24261260.20451181X-RAY DIFFRACTION95.61
6.77-40.230.26181150.19981196X-RAY DIFFRACTION94.18

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