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- PDB-7s5p: Crystal structure of SARS-CoV-2 B.1.351 variant receptor binding ... -

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Basic information

Entry
Database: PDB / ID: 7s5p
TitleCrystal structure of SARS-CoV-2 B.1.351 variant receptor binding domain in complex with neutralizing antibody CS23
Components
  • CS23 Heavy chain
  • CS23 Light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Coronavirus / Antibody / Fab / VOC / Beta / B.1.351 / Spike / RBD / 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 / receptor-mediated endocytosis of virus by host cell / membrane fusion / 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: 2.86 Å
AuthorsYuan, M. / Wilson, I.A.
Funding support2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923
Bavarian State Ministry for Education, Culture, Science and Arts01KI20271
CitationJournal: Science / Year: 2022
Title: SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies.
Authors: Reincke, S.M. / Yuan, M. / Kornau, H.C. / Corman, V.M. / van Hoof, S. / Sanchez-Sendin, E. / Ramberger, M. / Yu, W. / Hua, Y. / Tien, H. / Schmidt, M.L. / Schwarz, T. / Jeworowski, L.M. / ...Authors: Reincke, S.M. / Yuan, M. / Kornau, H.C. / Corman, V.M. / van Hoof, S. / Sanchez-Sendin, E. / Ramberger, M. / Yu, W. / Hua, Y. / Tien, H. / Schmidt, M.L. / Schwarz, T. / Jeworowski, L.M. / Brandl, S.E. / Rasmussen, H.F. / Homeyer, M.A. / Stoffler, L. / Barner, M. / Kunkel, D. / Huo, S. / Horler, J. / von Wardenburg, N. / Kroidl, I. / Eser, T.M. / Wieser, A. / Geldmacher, C. / Hoelscher, M. / Ganzer, H. / Weiss, G. / Schmitz, D. / Drosten, C. / Pruss, H. / Wilson, I.A. / Kreye, J.
History
DepositionSep 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
H: CS23 Heavy chain
L: CS23 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,61019
Polymers72,0163
Non-polymers1,59416
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-162 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.898, 145.898, 111.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody CS23 Heavy chain


Mass: 23244.070 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 CS23 Light chain


Mass: 22642.850 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: 26129.410 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
#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

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Non-polymers , 3 types, 44 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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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: 4.14 Å3/Da / Density % sol: 70.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 1.6 M ammonium sulfate and 0.1 M bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.86→50 Å / Num. obs: 28522 / % possible obs: 100 % / Redundancy: 24.5 % / Biso Wilson estimate: 48.78 Å2 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.052 / Rrim(I) all: 0.262 / Χ2: 0.47 / Net I/σ(I): 2.3 / Num. measured all: 697930
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.86-2.9114.81.34613860.5660.3521.3950.4299.5
2.91-2.9617.61.18913980.6870.2871.2250.424100
2.96-3.02201.05613940.8270.241.0840.422100
3.02-3.0823.41.02613960.8730.2151.0490.422100
3.08-3.1525.30.92413950.9160.1860.9430.428100
3.15-3.2225.70.77514230.9340.1550.7910.433100
3.22-3.325.10.63413890.9510.1290.6480.439100
3.3-3.3927.30.55314290.9730.1070.5630.442100
3.39-3.4927.20.45313930.9820.0880.4610.458100
3.49-3.626.90.36914050.990.0720.3760.461100
3.6-3.7326.40.31814140.990.0630.3240.476100
3.73-3.88250.26814100.9930.0540.2730.474100
3.88-4.06260.20714300.9950.0410.2110.489100
4.06-4.27260.17714250.9970.0350.180.492100
4.27-4.5425.70.13514210.9980.0270.1370.52100
4.54-4.89270.13414470.9980.0260.1360.509100
4.89-5.38260.13214350.9980.0260.1350.494100
5.38-6.1624.90.14114590.9970.0280.1430.476100
6.16-7.7525.40.12714780.9980.0260.130.482100
7.75-5023.40.06815950.9990.0140.0690.572100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XC2

6xc2


Resolution: 2.86→49.21 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 2000 7.03 %
Rwork0.2083 26467 -
obs0.211 28467 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.86 Å2 / Biso mean: 52.6733 Å2 / Biso min: 14.51 Å2
Refinement stepCycle: final / Resolution: 2.86→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4656 0 87 29 4772
Biso mean--80.49 34.12 -
Num. residues----616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.86-2.930.38511380.33061833197199
2.93-3.010.32851400.296518451985100
3.01-3.10.33481410.269918602001100
3.1-3.20.31451400.249218571997100
3.2-3.310.30451410.245318642005100
3.31-3.450.25281410.231818692010100
3.45-3.60.27461420.214618772019100
3.6-3.790.22261400.209518591999100
3.79-4.030.25131440.183919022046100
4.03-4.340.19871430.166418862029100
4.34-4.780.18651430.152418952038100
4.78-5.470.21251450.167719212066100
5.47-6.890.24921470.200719452092100
6.89-49.210.22671550.223420542209100

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