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- PDB-9epa: Crystal structure of DARPin NY_1 -

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Basic information

Entry
Database: PDB / ID: 9epa
TitleCrystal structure of DARPin NY_1
ComponentsDARPin NY_1
KeywordsIMMUNE SYSTEM / DARPin targeting MHC molecules in complex with tumor-associated peptide antigens
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsSchulte, T. / Sandalova, T. / Walser, M. / Mueller, S. / Venetz, N. / Achour, A.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Cancerfonden Sweden
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Development of highly specific and potent HLA/peptide-targeting DARPin T cell engagers
Authors: Venetz, N. / Schulte, T. / Mueller, S. / Wallden, K. / Fischer, S. / Kadri, N. / Paladino, M. / Pina, N. / Radom, F. / Villemagne, D. / Bruckmaier, S. / Cornelius, A. / Hospodarsch, T. / ...Authors: Venetz, N. / Schulte, T. / Mueller, S. / Wallden, K. / Fischer, S. / Kadri, N. / Paladino, M. / Pina, N. / Radom, F. / Villemagne, D. / Bruckmaier, S. / Cornelius, A. / Hospodarsch, T. / Sun, R. / Chambers, B.J. / Carroni, M. / Levitsky, V. / Sandalova, T. / Walser, M. / Achour, A.
History
DepositionMar 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DARPin NY_1


Theoretical massNumber of molelcules
Total (without water)18,5961
Polymers18,5961
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7310 Å2
Unit cell
Length a, b, c (Å)106.558, 43.284, 32.409
Angle α, β, γ (deg.)90.000, 93.784, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein DARPin NY_1


Mass: 18596.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.01 Å3/Da / Density % sol: 38.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: NY_1/HLA-A0201/NY-ESO1157-165(9V) complex was concentrated to 10 mg/mL in 20 mM HEPES, 10% glycerol, 300 mM NaCl pH 7.5. Crystallization was performed within the protein science facility at ...Details: NY_1/HLA-A0201/NY-ESO1157-165(9V) complex was concentrated to 10 mg/mL in 20 mM HEPES, 10% glycerol, 300 mM NaCl pH 7.5. Crystallization was performed within the protein science facility at Karolinska Institutet (https://ki.se/en/mbb/psf-mx). Crystals of NY_1 alone were obtained in condition 1-48 (pH 8.5; 0.12 M alcohol mix; 0.1 M buffer system 3; 37.5% (v/v) MPD_P1K_P3350) of the Morpheus screen (Molecular Dimensions Ltd.). For condition screening, the Mosquito robot was used to setup 1:2, 1:1 and 2:1 drop ratios in 96-well sitting-drop iQ TTP Labtech plates (TTP Labtech).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9688 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 1.76→28.48 Å / Num. obs: 14698 / % possible obs: 99.55 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.22 Å2 / CC1/2: 0.982 / Net I/σ(I): 6.53
Reflection shellResolution: 1.761→1.824 Å / Num. unique obs: 14698 / CC1/2: 0.796

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Cootmodel building
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→28.48 Å / SU ML: 0.2228 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.3856
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2154 1460 9.94 %
Rwork0.1832 13232 -
obs0.1864 14692 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.21 Å2
Refinement stepCycle: LAST / Resolution: 1.76→28.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1154 0 0 122 1276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731168
X-RAY DIFFRACTIONf_angle_d0.92321581
X-RAY DIFFRACTIONf_chiral_restr0.0535193
X-RAY DIFFRACTIONf_plane_restr0.007206
X-RAY DIFFRACTIONf_dihedral_angle_d4.6606160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.820.29141430.23511257X-RAY DIFFRACTION94.28
1.82-1.90.2841490.24221315X-RAY DIFFRACTION99.8
1.9-1.980.24771440.21311305X-RAY DIFFRACTION99.93
1.98-2.090.23881430.19711322X-RAY DIFFRACTION100
2.09-2.220.25431520.1991335X-RAY DIFFRACTION99.93
2.22-2.390.2311360.19381320X-RAY DIFFRACTION100
2.39-2.630.22011450.16741335X-RAY DIFFRACTION99.93
2.63-3.010.2061430.18251336X-RAY DIFFRACTION100
3.01-3.790.19681530.16921332X-RAY DIFFRACTION99.87
3.79-28.480.17461520.16191375X-RAY DIFFRACTION99.54

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