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- PDB-8sdg: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 8sdg
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.43
Components
  • Neutralizing antibody CC25.43 heavy chain
  • Neutralizing antibody CC25.43 light chain
  • Spike protein S1
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / coronavirus / antibody
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 / 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 / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsYuan, M. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI170928 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)CHAVD UM1 AI44462 United States
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Biorxiv / Year: 2023
Title: Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift.
Authors: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R.N. / Torres, J.L. / He, W.T. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / ...Authors: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R.N. / Torres, J.L. / He, W.T. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / Avillion, G. / Vo, A.L. / Li, X. / Makhdoomi, M. / Feng, Z. / Zhu, X. / Peng, L. / Nemazee, D. / Safonova, Y. / Briney, B. / Ward, A.B. / Burton, D.R. / Wilson, I.A. / Andrabi, R.
History
DepositionApr 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Neutralizing antibody CC25.43 heavy chain
I: Neutralizing antibody CC25.43 light chain
C: Spike protein S1
A: Neutralizing antibody CC25.43 heavy chain
B: Neutralizing antibody CC25.43 light chain
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,6257
Polymers141,4046
Non-polymers2211
Water00
1
G: Neutralizing antibody CC25.43 heavy chain
I: Neutralizing antibody CC25.43 light chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9234
Polymers70,7023
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Neutralizing antibody CC25.43 heavy chain
B: Neutralizing antibody CC25.43 light chain
D: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)70,7023
Polymers70,7023
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)311.948, 83.786, 74.150
Angle α, β, γ (deg.)90.00, 100.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Neutralizing antibody CC25.43 heavy chain


Mass: 24064.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Neutralizing antibody CC25.43 light chain


Mass: 23533.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Spike protein S1


Mass: 23104.867 Da / Num. of mol.: 2 / 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
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: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Li-chloride, 10% PEG-6000, and 0.1 M citric acid pH 4.0

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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: Nov 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.71→153.213 Å / Num. obs: 47774 / % possible obs: 93.4 % / Redundancy: 5.2 % / CC1/2: 0.995 / Net I/σ(I): 7.8
Reflection shellResolution: 2.71→2.76 Å / Num. unique obs: 2451 / CC1/2: 0.495

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→72.84 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3076 2385 5.01 %
Rwork0.2546 --
obs0.2572 47628 93.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→72.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9522 0 14 0 9536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049759
X-RAY DIFFRACTIONf_angle_d0.69713284
X-RAY DIFFRACTIONf_dihedral_angle_d4.5171348
X-RAY DIFFRACTIONf_chiral_restr0.0461481
X-RAY DIFFRACTIONf_plane_restr0.0051718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.770.39841840.37122672X-RAY DIFFRACTION96
2.77-2.830.37821470.34412840X-RAY DIFFRACTION100
2.83-2.90.39061630.32942809X-RAY DIFFRACTION100
2.9-2.970.37621830.30042805X-RAY DIFFRACTION99
2.97-3.050.39541580.29762806X-RAY DIFFRACTION100
3.05-3.140.31751540.29092793X-RAY DIFFRACTION99
3.14-3.240.38541290.28242868X-RAY DIFFRACTION99
3.24-3.350.351490.27212815X-RAY DIFFRACTION99
3.35-3.390.3422370.2827720X-RAY DIFFRACTION98
3.49-3.640.38171340.31132613X-RAY DIFFRACTION98
3.68-3.840.32891210.29332269X-RAY DIFFRACTION96
3.84-4.080.34981240.26122820X-RAY DIFFRACTION98
4.08-4.40.24051020.22972915X-RAY DIFFRACTION100
4.4-4.840.2741480.21742874X-RAY DIFFRACTION100
4.84-5.540.27281520.21272847X-RAY DIFFRACTION100
5.54-6.980.28611430.25252868X-RAY DIFFRACTION99
6.98-72.840.24191570.21692909X-RAY DIFFRACTION98

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