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- PDB-7np1: Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Co... -

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Basic information

Entry
Database: PDB / ID: 7np1
TitleCrystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-360
Components
  • Immunoblobulin light chain
  • Immunoglobulin gamma-1 heavy chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / Antibody Immune System
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / 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 / symbiont entry into host cell / 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 / 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 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 / 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: 2.8 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
DepositionFeb 26, 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 1.2Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
B: Spike protein S1
C: Spike protein S1
D: Spike protein S1
H: Immunoglobulin gamma-1 heavy chain
I: Immunoglobulin gamma-1 heavy chain
J: Immunoglobulin gamma-1 heavy chain
K: Immunoglobulin gamma-1 heavy chain
L: Immunoblobulin light chain
M: Immunoblobulin light chain
N: Immunoblobulin light chain
O: Immunoblobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,20116
Polymers293,02412
Non-polymers1,1774
Water1,27971
1
A: Spike protein S1
H: Immunoglobulin gamma-1 heavy chain
L: Immunoblobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6234
Polymers73,2563
Non-polymers3671
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
I: Immunoglobulin gamma-1 heavy chain
M: Immunoblobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4774
Polymers73,2563
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Spike protein S1
J: Immunoglobulin gamma-1 heavy chain
N: Immunoblobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6234
Polymers73,2563
Non-polymers3671
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Spike protein S1
K: Immunoglobulin gamma-1 heavy chain
O: Immunoblobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4774
Polymers73,2563
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.049, 107.899, 181.628
Angle α, β, γ (deg.)90.000, 99.448, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Antibody , 2 types, 8 molecules HIJKLMNO

#2: Antibody
Immunoglobulin gamma-1 heavy chain


Mass: 23397.207 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
Immunoblobulin light chain


Mass: 23759.311 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 75 molecules ABCD

#1: Protein
Spike protein S1


Mass: 26099.357 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 4 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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: 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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Details

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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 16% PEG3350 0.2 M ammonium 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: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2.8→48.33 Å / Num. obs: 85521 / % possible obs: 99.75 % / Redundancy: 2 % / Biso Wilson estimate: 66.65 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.0629 / Net I/σ(I): 5.79
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 8446 / CC1/2: 0.494

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Processing

Software
NameVersionClassification
PDB-REDOv1.0refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BNV

7bnv


Resolution: 2.8→48.28 Å / SU ML: 0.4344 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.2544
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.281 8471 9.92 %RANDOM
Rwork0.2321 76908 --
obs0.2369 85379 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.92 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18679 0 76 71 18826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003919212
X-RAY DIFFRACTIONf_angle_d0.802226106
X-RAY DIFFRACTIONf_chiral_restr0.04892907
X-RAY DIFFRACTIONf_plane_restr0.00643347
X-RAY DIFFRACTIONf_dihedral_angle_d6.46042701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.37932610.32272556X-RAY DIFFRACTION98.22
2.83-2.870.36992870.31562485X-RAY DIFFRACTION99.46
2.87-2.90.39622660.3042589X-RAY DIFFRACTION99.62
2.9-2.940.36352580.30112591X-RAY DIFFRACTION99.55
2.94-2.980.37162930.29492507X-RAY DIFFRACTION99.79
2.98-3.020.35093140.28582524X-RAY DIFFRACTION99.79
3.02-3.060.34962630.28972594X-RAY DIFFRACTION99.86
3.06-3.110.36912820.30192500X-RAY DIFFRACTION99.86
3.11-3.150.38412860.28832589X-RAY DIFFRACTION99.93
3.15-3.210.33512870.26792556X-RAY DIFFRACTION99.96
3.21-3.260.32243170.27862542X-RAY DIFFRACTION100
3.26-3.320.32852580.26262528X-RAY DIFFRACTION99.86
3.32-3.380.32942730.25162590X-RAY DIFFRACTION99.86
3.38-3.450.30292680.24862560X-RAY DIFFRACTION100
3.45-3.530.28413050.24562538X-RAY DIFFRACTION99.93
3.53-3.610.29552690.23952577X-RAY DIFFRACTION99.89
3.61-3.70.31722780.24672557X-RAY DIFFRACTION99.89
3.7-3.80.29253140.23852540X-RAY DIFFRACTION99.86
3.8-3.910.29572800.23182578X-RAY DIFFRACTION99.86
3.91-4.040.28862700.23042563X-RAY DIFFRACTION99.96
4.04-4.180.2772810.21372558X-RAY DIFFRACTION99.96
4.18-4.350.2493050.19772552X-RAY DIFFRACTION99.97
4.35-4.550.24492930.22582X-RAY DIFFRACTION100
4.55-4.790.2562590.19142585X-RAY DIFFRACTION99.93
4.79-5.090.22372820.19712568X-RAY DIFFRACTION99.93
5.09-5.480.24332730.20172574X-RAY DIFFRACTION99.96
5.48-6.030.24992500.21542640X-RAY DIFFRACTION99.97
6.03-6.90.2762920.2242568X-RAY DIFFRACTION99.83
6.9-8.680.25093150.21332588X-RAY DIFFRACTION99.76
8.69-48.280.23912920.2332629X-RAY DIFFRACTION98.65

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