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- PDB-6ias: structure of human NKp46 in complex with antibody NKp46-1 and NKp46-4 -

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Basic information

Entry
Database: PDB / ID: 6ias
Titlestructure of human NKp46 in complex with antibody NKp46-1 and NKp46-4
Components
  • Fab NKp46-1 heavy chain
  • Fab NKp46-1 light chain
KeywordsIMMUNE SYSTEM / THERAPEUTIC ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsRoussel, A. / Amigues, B.
CitationJournal: Cell / Year: 2019
Title: Multifunctional Natural Killer Cell Engagers Targeting NKp46 Trigger Protective Tumor Immunity.
Authors: Gauthier, L. / Morel, A. / Anceriz, N. / Rossi, B. / Blanchard-Alvarez, A. / Grondin, G. / Trichard, S. / Cesari, C. / Sapet, M. / Bosco, F. / Rispaud-Blanc, H. / Guillot, F. / Cornen, S. / ...Authors: Gauthier, L. / Morel, A. / Anceriz, N. / Rossi, B. / Blanchard-Alvarez, A. / Grondin, G. / Trichard, S. / Cesari, C. / Sapet, M. / Bosco, F. / Rispaud-Blanc, H. / Guillot, F. / Cornen, S. / Roussel, A. / Amigues, B. / Habif, G. / Caraguel, F. / Arrufat, S. / Remark, R. / Romagne, F. / Morel, Y. / Narni-Mancinelli, E. / Vivier, E.
History
DepositionNov 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev / database_PDB_rev_record
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab NKp46-1 heavy chain
L: Fab NKp46-1 light chain


Theoretical massNumber of molelcules
Total (without water)46,4792
Polymers46,4792
Non-polymers00
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-23 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.657, 61.101, 84.138
Angle α, β, γ (deg.)90.000, 105.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab NKp46-1 heavy chain


Mass: 23233.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab NKp46-1 light chain


Mass: 23244.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MMT pH8.5-9.5, 20-30%(w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.725→37.25 Å / Num. obs: 50086 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 32.64 Å2 / Net I/σ(I): 8.8
Reflection shellResolution: 1.725→1.82 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→36.76 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2316 4.8 %RANDOM
Rwork0.195 ---
obs0.197 48206 100 %-
Displacement parametersBiso max: 134.01 Å2 / Biso mean: 41.55 Å2 / Biso min: 17.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.5558 Å20 Å20.0836 Å2
2--0.1786 Å20 Å2
3----0.7343 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.75→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 0 399 3642
Biso mean---48.18 -
Num. residues----428
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1095SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes488HARMONIC5
X-RAY DIFFRACTIONt_it3335HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion446SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4000SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3335HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4540HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.75
X-RAY DIFFRACTIONt_other_torsion15.1
LS refinement shellResolution: 1.75→1.79 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 176 4.96 %
Rwork0.257 3369 -
all0.257 3545 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8107-0.1596-0.9530.51160.01732.63630.03320.01150.07820.01410.05340.1301-0.1236-0.2314-0.0866-0.1074-0.0043-0.0079-0.0970.0176-0.086110.7752-3.027515.149
21.38660.95730.32670.9467-0.27740.59560.2795-0.34210.08690.253-0.16930-0.04870.0536-0.1101-0.1201-0.056-0.0061-0.1375-0.012-0.218622.40882.593528.3487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|* }H1 - 220
2X-RAY DIFFRACTION2{ L|* }L1 - 211

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