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- PDB-7y3n: Crystal structure of SARS-CoV receptor binding domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 7y3n
TitleCrystal structure of SARS-CoV receptor binding domain in complex with human antibody BIOLS56
Components
  • Heavy chain of BIOLS56
  • Light chain of BIOLS56
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / symbiont-mediated-mediated suppression of host tetherin activity / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / SARS-CoV-1 activates/modulates innate immune responses / symbiont-mediated-mediated suppression of host tetherin activity / membrane fusion / 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 / 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 / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsRao, X. / Chai, Y. / Wu, Y. / Gao, F.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010202 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.
Authors: Rao, X. / Zhao, R. / Tong, Z. / Guo, S. / Peng, W. / Liu, K. / Li, S. / Wu, L. / Tong, J. / Chai, Y. / Han, P. / Wang, F. / Jia, P. / Li, Z. / Zhao, X. / Li, D. / Zhang, R. / Zhang, X. / ...Authors: Rao, X. / Zhao, R. / Tong, Z. / Guo, S. / Peng, W. / Liu, K. / Li, S. / Wu, L. / Tong, J. / Chai, Y. / Han, P. / Wang, F. / Jia, P. / Li, Z. / Zhao, X. / Li, D. / Zhang, R. / Zhang, X. / Zou, W. / Li, W. / Wang, Q. / Gao, G.F. / Wu, Y. / Dai, L. / Gao, F.
History
DepositionJun 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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: Heavy chain of BIOLS56
L: Light chain of BIOLS56
B: Spike protein S1
C: Heavy chain of BIOLS56
D: Light chain of BIOLS56
E: Spike protein S1
F: Heavy chain of BIOLS56
G: Light chain of BIOLS56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,69511
Polymers223,9049
Non-polymers7922
Water00
1
A: Spike protein S1
H: Heavy chain of BIOLS56
L: Light chain of BIOLS56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2054
Polymers74,6353
Non-polymers5711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
C: Heavy chain of BIOLS56
D: Light chain of BIOLS56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8564
Polymers74,6353
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Spike protein S1
F: Heavy chain of BIOLS56
G: Light chain of BIOLS56


Theoretical massNumber of molelcules
Total (without water)74,6353
Polymers74,6353
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.483, 159.018, 175.990
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: Protein Spike protein S1


Mass: 25863.234 Da / Num. of mol.: 3 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Gene: S, 2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P59594
#2: Antibody Heavy chain of BIOLS56


Mass: 25340.391 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Light chain of BIOLS56


Mass: 23430.943 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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
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: 3.8 Å3/Da / Density % sol: 67.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 20% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.9, 20% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.97→50 Å / Num. obs: 64593 / % possible obs: 99.3 % / Redundancy: 12.5 % / Biso Wilson estimate: 55.17 Å2 / Rmerge(I) obs: 0.281 / Net I/σ(I): 9.1
Reflection shellResolution: 2.97→3.11 Å / Rmerge(I) obs: 0.898 / Num. unique obs: 64593

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.13-2998refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG, 4TSA

6lzg

4tsa


Resolution: 2.97→47.39 Å / SU ML: 0.3884 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8357
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2628 3179 4.98 %
Rwork0.2204 60625 -
obs0.2226 63804 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.95 Å2
Refinement stepCycle: LAST / Resolution: 2.97→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14568 0 52 0 14620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005315000
X-RAY DIFFRACTIONf_angle_d0.931920437
X-RAY DIFFRACTIONf_chiral_restr0.06892272
X-RAY DIFFRACTIONf_plane_restr0.00632615
X-RAY DIFFRACTIONf_dihedral_angle_d17.00235334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.020.3299950.31571894X-RAY DIFFRACTION70.99
3.02-3.070.40151240.3172499X-RAY DIFFRACTION93.28
3.07-3.120.35541260.29962558X-RAY DIFFRACTION94.64
3.12-3.170.38891510.30672581X-RAY DIFFRACTION97.26
3.17-3.230.3441440.29152597X-RAY DIFFRACTION98.28
3.23-3.290.36631340.28582649X-RAY DIFFRACTION98.65
3.29-3.360.30661360.2662634X-RAY DIFFRACTION98.54
3.36-3.430.29751310.2642675X-RAY DIFFRACTION98.7
3.43-3.510.30831670.26122603X-RAY DIFFRACTION98.37
3.51-3.60.28271390.24672663X-RAY DIFFRACTION98.52
3.6-3.690.26661360.24852653X-RAY DIFFRACTION98.97
3.69-3.80.28841380.23942647X-RAY DIFFRACTION98.51
3.8-3.920.29861360.23622645X-RAY DIFFRACTION98.55
3.92-4.060.28981390.21652695X-RAY DIFFRACTION99.02
4.06-4.230.24391430.20032671X-RAY DIFFRACTION99.29
4.23-4.420.20551350.17752710X-RAY DIFFRACTION99.51
4.42-4.650.19691430.17692697X-RAY DIFFRACTION99.82
4.65-4.940.20351280.16732716X-RAY DIFFRACTION99.79
4.94-5.320.21341460.16912706X-RAY DIFFRACTION99.86
5.33-5.860.23281410.18272762X-RAY DIFFRACTION99.79
5.86-6.710.2511340.20492750X-RAY DIFFRACTION99.86
6.71-8.440.2321430.19952789X-RAY DIFFRACTION99.9
8.44-47.390.22951700.2072831X-RAY DIFFRACTION97.98

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