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- PDB-7u2e: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7u2e
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADI-55688
Components
  • ADI-55688 heavy chain
  • ADI-55688 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 / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 ...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. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / 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: 2.85 Å
AuthorsYuan, M. / Zhu, X. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: ADI-55688 heavy chain
L: ADI-55688 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,12913
Polymers70,0433
Non-polymers1,08610
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-147 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.006, 101.006, 79.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#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
#2: Antibody ADI-55688 heavy chain


Mass: 24004.758 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 ADI-55688 light chain


Mass: 22933.352 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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: 0.08 M sodium acetate, pH 3.8, 1.6 M ammonium sulfate, and 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 18846 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 70.03 Å2 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.051 / Rrim(I) all: 0.154 / Χ2: 0.975 / Net I/σ(I): 5.4 / Num. measured all: 166809
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.97.31.3189120.590.5131.4170.40699.9
2.9-2.958.21.0849560.7220.41.1570.398100
2.95-3.018.60.9779140.7830.351.0390.414100
3.01-3.078.80.7819520.8730.2770.830.43100
3.07-3.148.70.6849470.8980.2440.7280.43100
3.14-3.218.40.539170.930.1920.5640.46100
3.21-3.297.90.399420.9430.1470.4180.50799.9
3.29-3.389.50.3329290.9680.1140.3510.555100
3.38-3.489.50.299620.9730.0990.3070.595100
3.48-3.599.70.2319090.9810.0780.2440.682100
3.59-3.729.40.1969490.9840.0670.2070.741100
3.72-3.879.30.1639420.9880.0560.1720.86100
3.87-4.049.20.149460.9890.0490.1480.99699.9
4.04-4.269.20.1169310.9930.040.1231.311100
4.26-4.528.80.0999480.9940.0350.1051.533100
4.52-4.877.70.0919300.9930.0340.0971.551100
4.87-5.369.60.099630.9940.0310.0951.51999.9
5.36-6.149.60.099580.9960.0310.0951.465100
6.14-7.739.20.0849510.9960.0290.0891.768100
7.73-508.40.0639880.9970.0230.0672.61699.7

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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: 7MF1

7mf1


Resolution: 2.85→45.17 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2844 1882 10 %
Rwork0.2541 16939 -
obs0.2572 18821 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.96 Å2 / Biso mean: 65.3914 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.85→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4765 0 59 0 4824
Biso mean--58.62 --
Num. residues----628
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.930.40691420.38761240138296
2.93-3.010.33671430.344112751418100
3.01-3.110.40511430.341413121455100
3.11-3.220.36221470.324912981445100
3.22-3.350.35871420.325412851427100
3.35-3.50.35761530.313713281481100
3.51-3.690.36691470.279212961443100
3.69-3.920.31591440.275712981442100
3.92-4.220.27191440.243812921436100
4.23-4.650.21971450.200113211466100
4.65-5.320.22091410.212613271468100
5.32-6.70.23051460.235713131459100
6.7-45.170.25111450.209113541499100

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