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- PDB-9h8r: Crystal structure of Nkp46 in complex with a bicyclic peptide BCY... -

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Basic information

Entry
Database: PDB / ID: 9h8r
TitleCrystal structure of Nkp46 in complex with a bicyclic peptide BCY00016132
Components
  • Bicyclic peptide BCY00016132
  • Natural cytotoxicity triggering receptor 1
KeywordsIMMUNE SYSTEM / receptor / complex / bicyclic peptide
Function / homology
Function and homology information


regulation of natural killer cell mediated cytotoxicity / immune response-regulating signaling pathway / natural killer cell activation / SWI/SNF complex / cellular defense response / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signal transduction / plasma membrane
Similarity search - Function
: / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
2-AMINO-ETHANETHIOL / Chem-LFI / Natural cytotoxicity triggering receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPellegrino, S. / Carr, K. / Bezerra, G.A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Crystal structure of Nkp46 in complex with a bicyclic peptide BCY00016132
Authors: Pellegrino, S. / Bezerra, G.A.
History
DepositionOct 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Natural cytotoxicity triggering receptor 1
B: Bicyclic peptide BCY00016132
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3795
Polymers24,7482
Non-polymers6313
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.688, 74.688, 75.307
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Natural cytotoxicity triggering receptor 1 / Lymphocyte antigen 94 homolog / NK cell-activating receptor / Natural killer cell p46-related ...Lymphocyte antigen 94 homolog / NK cell-activating receptor / Natural killer cell p46-related protein / NK-p46 / NKp46 / hNKp46


Mass: 23025.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCR1, LY94 / Production host: Escherichia coli (E. coli) / References: UniProt: O76036
#2: Protein/peptide Bicyclic peptide BCY00016132


Mass: 1722.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 163 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DHL / 2-AMINO-ETHANETHIOL / 2,3-DESHYDROLANTHIONINE


Type: L-peptide linking / Mass: 77.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NS
#5: Chemical ChemComp-LFI / 1-[3,5-bis(3-bromanylpropanoyl)-1,3,5-triazinan-1-yl]-3-bromanyl-propan-1-one / Chemical crosslinker


Mass: 492.002 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18Br3N3O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1.0 M Lithium sulfate, 0.1 M Tris pH 8.5, 0.01 M nickel (II) chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→64.68 Å / Num. obs: 24029 / % possible obs: 99.6 % / Redundancy: 17.5 % / Rpim(I) all: 0.029 / Rrim(I) all: 0.129 / Net I/σ(I): 11.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 8.8 % / Num. unique obs: 1311 / Rpim(I) all: 0.505 / Rrim(I) all: 1.514

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→64.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.059 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23907 1081 4.5 %RANDOM
Rwork0.20763 ---
obs0.20901 22914 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.928 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å2-0.43 Å2-0 Å2
2---0.87 Å20 Å2
3---2.81 Å2
Refinement stepCycle: 1 / Resolution: 1.75→64.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 32 160 1790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121744
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161613
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.8542376
X-RAY DIFFRACTIONr_angle_other_deg0.5811.7343738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1065215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.6036.15413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97810274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02403
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4992.826821
X-RAY DIFFRACTIONr_mcbond_other2.3692.809816
X-RAY DIFFRACTIONr_mcangle_it3.4525.0491023
X-RAY DIFFRACTIONr_mcangle_other3.3275.0381022
X-RAY DIFFRACTIONr_scbond_it3.743.204923
X-RAY DIFFRACTIONr_scbond_other3.7383.206924
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4825.7211343
X-RAY DIFFRACTIONr_long_range_B_refined7.33736.297096
X-RAY DIFFRACTIONr_long_range_B_other7.33936.37096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 96 -
Rwork0.318 1679 -
obs--99.94 %

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