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- PDB-7u2d: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7u2d
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADG20
Components
  • ADG20 heavy chain
  • ADG20 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Coronavirus / Antibody / 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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
CITRIC ACID / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsZhu, X. / Yuan, M. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: A broad and potent neutralization epitope in SARS-related coronaviruses.
Authors: Yuan, M. / Zhu, X. / He, W.T. / Zhou, P. / Kaku, C.I. / Capozzola, T. / Zhu, C.Y. / Yu, X. / Liu, H. / Yu, W. / Hua, Y. / Tien, H. / Peng, L. / Song, G. / Cottrell, C.A. / Schief, W.R. / ...Authors: Yuan, M. / Zhu, X. / He, W.T. / Zhou, P. / Kaku, C.I. / Capozzola, T. / Zhu, C.Y. / Yu, X. / Liu, H. / Yu, W. / Hua, Y. / Tien, H. / Peng, L. / Song, G. / Cottrell, C.A. / Schief, W.R. / Nemazee, D. / Walker, L.M. / Andrabi, R. / Burton, D.R. / Wilson, I.A.
#1: Journal: Biorxiv / Year: 2022
Title: A broad and potent neutralization epitope in SARS-related coronaviruses.
Authors: Yuan, M. / Zhu, X. / He, W.T. / Zhou, P. / Kaku, C.I. / Capozzola, T. / Zhu, C.Y. / Yu, X. / Liu, H. / Yu, W. / Hua, Y. / Tien, H. / Peng, L. / Song, G. / Cottrell, C.A. / Schief, W.R. / ...Authors: Yuan, M. / Zhu, X. / He, W.T. / Zhou, P. / Kaku, C.I. / Capozzola, T. / Zhu, C.Y. / Yu, X. / Liu, H. / Yu, W. / Hua, Y. / Tien, H. / Peng, L. / Song, G. / Cottrell, C.A. / Schief, W.R. / Nemazee, D. / Walker, L.M. / Andrabi, R. / Burton, D.R. / Wilson, I.A.
History
DepositionFeb 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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: ADG20 heavy chain
L: ADG20 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,08610
Polymers70,1923
Non-polymers8947
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-88 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.083, 101.083, 80.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody ADG20 heavy chain


Mass: 24134.861 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 ADG20 light chain


Mass: 22952.312 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: 23104.867 Da / Num. of mol.: 1 / Fragment: Receptor binding domain, UNP residues 333-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 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, 40 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.16
Details: 0.1 M sodium citrate, pH 4.16 and 1.45 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 20610 / % possible obs: 97.6 % / Redundancy: 11.2 % / Biso Wilson estimate: 71.91 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.034 / Rrim(I) all: 0.119 / Χ2: 0.734 / Net I/σ(I): 6.4 / Num. measured all: 230397
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.816.50.98913570.6930.3831.0650.29998.1
2.81-2.887.70.89214080.7730.3250.9510.29999.5
2.88-2.968.60.75413820.860.2650.80.3299.4
2.96-3.058.40.5913860.9190.2140.6290.35399.9
3.05-3.1511.10.49314190.9640.1510.5160.36100
3.15-3.2612.90.38213770.9830.1090.3970.389100
3.26-3.3913.50.30714140.9890.0860.3190.435100
3.39-3.5513.50.27113800.9910.0760.2810.487100
3.55-3.738.20.2779920.9560.0910.2931.16669.9
3.73-3.9711.30.15813920.9950.0480.1660.65499.6
3.97-4.2712.40.09514080.9980.0280.0990.89499.6
4.27-4.711.70.07214020.9980.0220.0761.08599.9
4.7-5.3814.30.06614210.9990.0180.0681.054100
5.38-6.7813.80.06214310.9990.0170.0641.046100
6.78-5012.50.04614410.9990.0130.0481.62699

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MF1

7mf1


Resolution: 2.76→35.74 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 1027 4.99 %
Rwork0.2195 19559 -
obs0.2215 20586 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.02 Å2 / Biso mean: 72.145 Å2 / Biso min: 28.8 Å2
Refinement stepCycle: final / Resolution: 2.76→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 52 34 4862
Biso mean--116.96 55.8 -
Num. residues----628
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.76-2.90.42511230.3932797292098
2.9-3.080.33161570.306728433000100
3.08-3.320.34391420.282928482990100
3.32-3.640.32331500.27792632278295
3.66-4.180.26661510.20782655280694
4.18-5.270.2121380.160728833021100
5.27-35.740.20151660.191329013067100

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