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- PDB-7e3o: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7e3o
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody nCoV617
Components
  • Spike protein S1
  • nCoV617 Heigh Chain
  • nCoV617 Light Chain
KeywordsVIRAL PROTEIN / SARS-CoV-2 / S-RBD / RBS-C / native human monoclonal antibody / therapeutic antibody
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 / 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 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsChen, S.D. / Yang, M.
CitationJournal: Microbiol Spectr / Year: 2021
Title: Structural Basis of a Human Neutralizing Antibody Specific to the SARS-CoV-2 Spike Protein Receptor-Binding Domain.
Authors: Yang, M. / Li, J. / Huang, Z. / Li, H. / Wang, Y. / Wang, X. / Kang, S. / Huang, X. / Wu, C. / Liu, T. / Jia, Z. / Liang, J. / Yuan, X. / He, S. / Chen, X. / Zhou, Z. / Chen, Q. / Liu, S. / ...Authors: Yang, M. / Li, J. / Huang, Z. / Li, H. / Wang, Y. / Wang, X. / Kang, S. / Huang, X. / Wu, C. / Liu, T. / Jia, Z. / Liang, J. / Yuan, X. / He, S. / Chen, X. / Zhou, Z. / Chen, Q. / Liu, S. / Li, J. / Zheng, H. / Liu, X. / Li, K. / Yao, X. / Lang, B. / Liu, L. / Liao, H.X. / Chen, S.
History
DepositionFeb 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: nCoV617 Light Chain
H: nCoV617 Heigh Chain
R: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)69,3773
Polymers69,3773
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-36 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.093, 60.367, 77.296
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody nCoV617 Light Chain


Mass: 22551.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector HA-MCS-pcDNA3.1 (others)
#2: Antibody nCoV617 Heigh Chain


Mass: 24278.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector HA-MCS-pcDNA3.1 (others)
#3: Protein Spike protein S1


Mass: 22547.164 Da / Num. of mol.: 1 / Fragment: UNP residues 337-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: unidentified baculovirus / References: UniProt: P0DTC2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 152 mM NH4Cl, 22.8% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: SDMS / Detector: CMOS / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.51→40.67 Å / Num. obs: 25491 / % possible obs: 94.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.897 / Net I/σ(I): -0.6
Reflection shellResolution: 2.514→2.603 Å / Num. unique obs: 2495 / CC1/2: 0.868

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J, 7K8Z

6m0j

7k8z


Resolution: 2.51→40.67 Å / SU ML: 0.3431 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.0598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2589 1996 7.84 %
Rwork0.204 23468 -
obs0.2083 25464 94.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.17 Å2
Refinement stepCycle: LAST / Resolution: 2.51→40.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 0 63 4741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00974801
X-RAY DIFFRACTIONf_angle_d1.2146542
X-RAY DIFFRACTIONf_chiral_restr0.0667725
X-RAY DIFFRACTIONf_plane_restr0.0089842
X-RAY DIFFRACTIONf_dihedral_angle_d14.15666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.580.33091380.23991623X-RAY DIFFRACTION94.83
2.58-2.650.36431450.26171706X-RAY DIFFRACTION97.78
2.65-2.720.30811450.24871702X-RAY DIFFRACTION96.8
2.72-2.810.32051440.25321680X-RAY DIFFRACTION96.46
2.81-2.910.33131440.24781693X-RAY DIFFRACTION96.38
2.91-3.030.34751440.23881702X-RAY DIFFRACTION95.9
3.03-3.170.29741420.23961671X-RAY DIFFRACTION95.17
3.17-3.330.28241420.23091673X-RAY DIFFRACTION94.98
3.33-3.540.30041430.22571672X-RAY DIFFRACTION94.63
3.54-3.820.29031430.21081687X-RAY DIFFRACTION94.87
3.82-4.20.25821450.19191683X-RAY DIFFRACTION93.94
4.2-4.810.19761410.15861671X-RAY DIFFRACTION92.69
4.81-6.050.20681410.17081668X-RAY DIFFRACTION90.95
6.05-40.670.20841390.19091637X-RAY DIFFRACTION85.22
Refinement TLS params.Method: refined / Origin x: -17.2087125013 Å / Origin y: 8.26329743651 Å / Origin z: -6.48148426029 Å
111213212223313233
T0.474870565229 Å2-0.0121177394775 Å20.0189358203883 Å2-0.48066937301 Å2-0.0094058205698 Å2--0.457613974792 Å2
L1.06121900395 °20.190912061987 °20.726946367854 °2-0.19017607079 °20.112790840697 °2--0.545442535615 °2
S-0.00638252055348 Å °0.116984759717 Å °-0.06776808289 Å °0.00828757034323 Å °0.048553685888 Å °-0.0165248554962 Å °-0.0450550366404 Å °0.106107057303 Å °-0.000347990682264 Å °
Refinement TLS groupSelection details: all

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