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- PDB-7xnf: Structure of SARS-CoV-2 antibody P2C-1F11 with GX/P2V/2017 RBD -

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Basic information

Entry
Database: PDB / ID: 7xnf
TitleStructure of SARS-CoV-2 antibody P2C-1F11 with GX/P2V/2017 RBD
Components
  • P2C-1F11 Heavy Chain
  • P2C-1F11 Lambda chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / GX/P2V/2017 / RBD / antibody / P2C1-F11 / Fab
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to 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 / 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 (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)
Pangolin coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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
DepositionApr 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: P2C-1F11 Heavy Chain
L: P2C-1F11 Lambda chain
A: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)71,5833
Polymers71,5833
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-26 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.722, 85.440, 183.739
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 P2C-1F11 Heavy Chain


Mass: 23983.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody P2C-1F11 Lambda chain


Mass: 23361.846 Da / Num. of mol.: 1
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.: 1 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES monohydrate (pH 6.0), 20% w/v Polyethylene glycol monomethyl ether 2000

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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: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 22549 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 48.31 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 11.905
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.925 / Num. unique obs: 2186

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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: 7CDI

7cdi


Resolution: 2.79→41.61 Å / SU ML: 0.6908 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.7352
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3795 1062 4.96 %
Rwork0.3196 20370 -
obs0.3225 21432 95.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.25 Å2
Refinement stepCycle: LAST / Resolution: 2.79→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4446 0 0 19 4465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00234546
X-RAY DIFFRACTIONf_angle_d0.5016173
X-RAY DIFFRACTIONf_chiral_restr0.0455689
X-RAY DIFFRACTIONf_plane_restr0.0035790
X-RAY DIFFRACTIONf_dihedral_angle_d16.3591626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.920.52521110.44151795X-RAY DIFFRACTION68.93
2.92-3.070.40571300.38012465X-RAY DIFFRACTION94.36
3.07-3.270.42581430.3642614X-RAY DIFFRACTION99.32
3.27-3.520.50021180.39532651X-RAY DIFFRACTION99.35
3.52-3.870.39251470.37532609X-RAY DIFFRACTION99.39
3.87-4.430.37551440.3072675X-RAY DIFFRACTION99.61
4.43-5.580.30011350.2392719X-RAY DIFFRACTION99.72
5.58-41.610.31281340.26722842X-RAY DIFFRACTION99.57

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