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- PDB-7jmo: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7jmo
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-04
Components
  • COVA2-04 heavy chain
  • COVA2-04 light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / COVID-19 / RBD / Antibody / SARS / Spike
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / host cell surface receptor binding / endocytosis involved in viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral entry into host cell / viral envelope / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
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. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...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. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike receptor binding domain superfamily, coronavirus / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / 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 / 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: 2.359 Å
AuthorsWu, N.C. / Yuan, M. / Liu, H. / Zhu, X. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI139445 United States
Bill & Melinda Gates FoundationOPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110657
CitationJournal: Biorxiv / Year: 2020
Title: An alternative binding mode of IGHV3-53 antibodies to the SARS-CoV-2 receptor binding domain.
Authors: Wu, N.C. / Yuan, M. / Liu, H. / Lee, C.D. / Zhu, X. / Bangaru, S. / Torres, J.L. / Caniels, T.G. / Brouwer, P.J.M. / van Gils, M.J. / Sanders, R.W. / Ward, A.B. / Wilson, I.A.
History
DepositionAug 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S1
H: COVA2-04 heavy chain
L: COVA2-04 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8134
Polymers73,5923
Non-polymers2211
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)197.246, 84.678, 57.301
Angle α, β, γ (deg.)90.000, 99.580, 90.000
Int Tables number5
Space group name H-MC121

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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 COVA2-04 heavy chain


Mass: 24140.041 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 COVA2-04 light chain


Mass: 23356.893 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.: 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 / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 8.5% isopropanol 10% ethylene glycol 15% glycerol 0.085 M HEPES pH 7.5 17% 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: 0.97946 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: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 37264 / % possible obs: 97.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.072 / Rrim(I) all: 0.179 / Χ2: 1.354 / Net I/σ(I): 5.7 / Num. measured all: 206757
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.393.70.89816890.6770.471.020.43888.6
2.39-2.433.90.88317770.780.4490.9970.42593.2
2.43-2.484.20.8418900.7920.4180.9430.44297.1
2.48-2.534.50.89318270.7110.430.9950.43897.8
2.53-2.594.70.81218870.830.3880.9040.45798.8
2.59-2.655.10.82418650.7850.3820.9120.47798.7
2.65-2.715.40.73918820.8250.3340.8130.48897.6
2.71-2.795.50.67518490.8290.3070.7440.50498
2.79-2.875.10.56418170.8610.2690.6270.52194.9
2.87-2.9660.43418520.940.1910.4750.60196.8
2.96-3.076.40.33319030.9670.140.3620.69899.3
3.07-3.196.50.27318820.9750.1130.2960.8899.1
3.19-3.336.40.21418960.9770.090.2331.11498.9
3.33-3.516.30.17218840.9850.0730.1881.46498.5
3.51-3.736.10.14618820.9880.0630.161.79699.1
3.73-4.025.90.12518850.9870.0550.1372.19397.4
4.02-4.425.60.10218490.990.0470.1132.69595.2
4.42-5.066.50.09119050.9930.0390.13.06899.7
5.06-6.376.50.08919300.9940.0370.0972.77399.3
6.37-506.10.06819130.9960.030.0753.17496.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XC4
Resolution: 2.359→48.624 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 1814 4.87 %
Rwork0.1951 35410 -
obs0.1972 37224 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.29 Å2 / Biso mean: 51.852 Å2 / Biso min: 27.99 Å2
Refinement stepCycle: final / Resolution: 2.359→48.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4767 0 14 124 4905
Biso mean--30 49.22 -
Num. residues----622
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3591-2.42280.35771070.3134239185
2.4228-2.49410.32391500.2771274097
2.4941-2.57460.30031420.2539270198
2.5746-2.66660.27471250.2476275098
2.6666-2.77340.30251440.2374275698
2.7734-2.89960.25711320.239267795
2.8996-3.05250.30021550.2209271698
3.0525-3.24370.2651530.2107279599
3.2437-3.4940.22841330.1989276399
3.494-3.84550.23741350.1889279999
3.8455-4.40170.2111320.1662270096
4.4017-5.54440.18361600.14812800100
5.5444-48.6240.22351460.1785282297

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