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- PDB-8gz6: Crystal structure of neutralizing VHH P17 in complex with SARS-Co... -

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Basic information

Entry
Database: PDB / ID: 8gz6
TitleCrystal structure of neutralizing VHH P17 in complex with SARS-CoV-2 Alpha variant spike receptor-binding domain
ComponentsNanobody P17
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / spike RBD / nanobody / VHH / VIRAL PROTEIN
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsYamaguchi, K. / Anzai, I. / Maeda, R. / Moriguchi, M. / Watanabe, T. / Imura, A. / Takaori-Kondo, A. / Inoue, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJOP1861 Japan
Japan Agency for Medical Research and Development (AMED)JP20fk018517 Japan
Other governmentKYOTO Industrial Support Organization 21
CitationJournal: J.Biochem. / Year: 2023
Title: Structural insights into the rational design of a nanobody that binds with high affinity to the SARS-CoV-2 spike variant.
Authors: Yamaguchi, K. / Anzai, I. / Maeda, R. / Moriguchi, M. / Watanabe, T. / Imura, A. / Takaori-Kondo, A. / Inoue, T.
History
DepositionSep 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Nanobody P17
B: Nanobody P17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3527
Polymers27,1482
Non-polymers2045
Water4,702261
1
A: Nanobody P17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7074
Polymers13,5741
Non-polymers1333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nanobody P17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6453
Polymers13,5741
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.758, 32.113, 84.566
Angle α, β, γ (deg.)90.000, 93.960, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Antibody Nanobody P17


Mass: 13574.040 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris propane pH 8.5, 24.5% w/v polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.35→42.18 Å / Num. obs: 46794 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.32 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.042 / Net I/σ(I): 9.5
Reflection shellResolution: 1.35→1.37 Å / Num. unique obs: 2408 / CC1/2: 0.686 / Rrim(I) all: 0.885

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GZ5

8gz5


Resolution: 1.35→42.18 Å / SU ML: 0.1776 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.1923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1795 2274 4.86 %
Rwork0.1486 44499 -
obs0.1501 46773 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.39 Å2
Refinement stepCycle: LAST / Resolution: 1.35→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 8 261 2066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01041883
X-RAY DIFFRACTIONf_angle_d1.2172553
X-RAY DIFFRACTIONf_chiral_restr0.1113274
X-RAY DIFFRACTIONf_plane_restr0.0092335
X-RAY DIFFRACTIONf_dihedral_angle_d6.6213281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.33411380.26492801X-RAY DIFFRACTION99.97
1.38-1.410.27241380.23822759X-RAY DIFFRACTION99.38
1.41-1.450.26141570.21042751X-RAY DIFFRACTION99.76
1.45-1.490.26271540.19182774X-RAY DIFFRACTION99.66
1.49-1.530.24481340.17782817X-RAY DIFFRACTION99.63
1.53-1.580.2031270.1652774X-RAY DIFFRACTION99.69
1.58-1.640.22141510.16222751X-RAY DIFFRACTION99.01
1.64-1.70.24211400.15142794X-RAY DIFFRACTION99.53
1.7-1.780.20891450.14152779X-RAY DIFFRACTION99.39
1.78-1.870.20971260.13652781X-RAY DIFFRACTION98.64
1.87-1.990.1861450.13942765X-RAY DIFFRACTION98.05
1.99-2.140.17521320.1322770X-RAY DIFFRACTION98.17
2.14-2.360.21131270.14932781X-RAY DIFFRACTION98.38
2.36-2.70.17761480.152772X-RAY DIFFRACTION98.09
2.7-3.40.15881650.14432753X-RAY DIFFRACTION97.56
3.4-42.180.13941470.13872877X-RAY DIFFRACTION97.58

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