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- PDB-7xsw: Structure of SARS-CoV-2 antibody S309 with GX/P2V/2017 RBD -

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Basic information

Entry
Database: PDB / ID: 7xsw
TitleStructure of SARS-CoV-2 antibody S309 with GX/P2V/2017 RBD
Components
  • S309 Heavy Chain
  • S309 Lambda Chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / GX/P2V/2017 / RBD / antibody / S309 / Fab / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / 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 / membrane
Similarity search - Function
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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 glycoprotein S1, N-terminal domain, betacoronavirus-like ...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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus spike glycoprotein S1, receptor binding / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Pangolin coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsJia, Y.F. / Chai, Y. / Wang, Q.H. / Gao, G.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2022
Title: Cross-reaction of current available SARS-CoV-2 MAbs against the pangolin-origin coronavirus GX/P2V/2017.
Authors: Jia, Y. / Niu, S. / Hu, Y. / Chai, Y. / Zheng, A. / Su, C. / Wu, L. / Han, P. / Han, P. / Lu, D. / Liu, Z. / Yan, X. / Tian, D. / Chen, Z. / Qi, J. / Tian, W.X. / Wang, Q. / Gao, G.F.
History
DepositionMay 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 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
H: S309 Heavy Chain
L: S309 Lambda Chain
R: Spike protein S1
A: S309 Heavy Chain
B: S309 Lambda Chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,4027
Polymers145,8316
Non-polymers5711
Water00
1
H: S309 Heavy Chain
L: S309 Lambda Chain
R: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4864
Polymers72,9163
Non-polymers5711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-15 kcal/mol
Surface area29320 Å2
MethodPISA
2
A: S309 Heavy Chain
B: S309 Lambda Chain
C: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)72,9163
Polymers72,9163
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-29 kcal/mol
Surface area29290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.639, 73.599, 105.615
Angle α, β, γ (deg.)110.527, 92.075, 97.049
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Antibody S309 Heavy Chain


Mass: 25386.365 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 S309 Lambda Chain


Mass: 23291.777 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 / S glycoprotein / E2 / Peplomer protein


Mass: 24237.365 Da / Num. of mol.: 2 / Fragment: BetaCoV S1-CTD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pangolin coronavirus / Production host: Homo sapiens (human) / References: UniProt: A0A6G6A2Q2
#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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
Has ligand of interestY
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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium chloride hexahydrate, 0.1M MES (pH 6.0), 20% w/v PEG 6000

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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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 40975 / % possible obs: 89 % / Redundancy: 4.94 % / Rrim(I) all: 3.421 / Net I/σ(I): 1.9
Reflection shellResolution: 3.3→3.5 Å / Num. unique obs: 6611 / Rrim(I) all: 3.303

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R6X

7r6x


Resolution: 3.3→48.54 Å / SU ML: 0.663 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.6184
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3216 1999 9.21 %
Rwork0.2766 19704 -
obs0.2808 21703 94.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.49 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9555 0 38 0 9593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00229817
X-RAY DIFFRACTIONf_angle_d0.543413344
X-RAY DIFFRACTIONf_chiral_restr0.04371492
X-RAY DIFFRACTIONf_plane_restr0.00381708
X-RAY DIFFRACTIONf_dihedral_angle_d14.52513495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.390.4031290.37891337X-RAY DIFFRACTION89.66
3.39-3.480.4531520.34711462X-RAY DIFFRACTION97.4
3.48-3.580.3891540.34691400X-RAY DIFFRACTION96.76
3.58-3.690.36731400.32241413X-RAY DIFFRACTION95.33
3.69-3.830.38821270.32541392X-RAY DIFFRACTION94.11
3.83-3.980.37681550.31911447X-RAY DIFFRACTION97.33
3.98-4.160.34631550.28941458X-RAY DIFFRACTION96.76
4.16-4.380.32771330.27821408X-RAY DIFFRACTION95.71
4.38-4.650.29151350.24741419X-RAY DIFFRACTION95.63
4.65-5.010.28681500.241372X-RAY DIFFRACTION91.69
5.01-5.520.30161480.25221428X-RAY DIFFRACTION96.87
5.52-6.310.30371390.25671424X-RAY DIFFRACTION96.72
6.31-7.950.32381380.26281385X-RAY DIFFRACTION92.7
7.95-48.540.22621440.22031359X-RAY DIFFRACTION92.04

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