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- PDB-9lrh: Killer immunoglobulin receptor KIR2DL2 in complex with KIR2DL2_KI... -

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Basic information

Entry
Database: PDB / ID: 9lrh
TitleKiller immunoglobulin receptor KIR2DL2 in complex with KIR2DL2_KIR2DL2/3 agonist 61-scFv
Components
  • KIR2DL2_KIR2DL2/3 agonist 61 scFV
  • Killer cell immunoglobulin-like receptor 2DL2
KeywordsIMMUNE SYSTEM / KIR / NATURAL KILLER RECEPTOR / INHIBITORY RECEPTOR / 2DL2 / IMMUNOGLOBULIN
Function / homology
Function and homology information


immune response-regulating signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / plasma membrane
Similarity search - Function
: / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Killer cell immunoglobulin-like receptor 2DL2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsNishikawa, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2025
Title: Selective agonists of KIR and NKG2A to evade missing self response of natural killer cells.
Authors: Hiura, S. / Kuwasaki, Y. / Nishikawa, Y. / Kimura, T. / Yoshida, S. / Nakayama, M. / Makino, T. / Ueno, S.
History
DepositionJan 31, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Killer cell immunoglobulin-like receptor 2DL2
H: KIR2DL2_KIR2DL2/3 agonist 61 scFV
L: KIR2DL2_KIR2DL2/3 agonist 61 scFV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4025
Polymers75,9603
Non-polymers4422
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-16 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.855, 98.855, 403.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Killer cell immunoglobulin-like receptor 2DL2 / CD158 antigen-like family member B1 / Natural killer-associated transcript 6 / NKAT-6 / p58 natural ...CD158 antigen-like family member B1 / Natural killer-associated transcript 6 / NKAT-6 / p58 natural killer cell receptor clone CL-43 / p58 NK receptor CL-43


Mass: 23234.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR2DL2, CD158B1, NKAT6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P43627
#2: Antibody KIR2DL2_KIR2DL2/3 agonist 61 scFV


Mass: 26362.385 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
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: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 100mM BIS-TRIS propane pH7.0, 29% Tacsimate pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→49.43 Å / Num. obs: 14337 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.058 / Rrim(I) all: 0.217 / Χ2: 1 / Net I/σ(I): 9.8 / Num. measured all: 193259
Reflection shellResolution: 3.4→3.67 Å / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 3.364 / Num. measured all: 40580 / Num. unique obs: 2882 / CC1/2: 0.589 / Rpim(I) all: 0.92 / Rrim(I) all: 3.489 / Χ2: 0.97 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DL2

2dl2


Resolution: 3.4→44.38 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 706 4.94 %
Rwork0.2267 --
obs0.228 14289 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3241 0 28 5 3274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.522
X-RAY DIFFRACTIONf_dihedral_angle_d10.7981202
X-RAY DIFFRACTIONf_chiral_restr0.042504
X-RAY DIFFRACTIONf_plane_restr0.004586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.660.42631140.38092642X-RAY DIFFRACTION99
3.66-4.030.34541380.292671X-RAY DIFFRACTION100
4.03-4.610.24741600.19542666X-RAY DIFFRACTION100
4.61-5.810.21831440.20192741X-RAY DIFFRACTION100
5.81-44.380.23771500.21772863X-RAY DIFFRACTION99
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)
14.6687-2.2724-4.82286.24631.65497.642-0.91190.96380.75370.34540.48122.30781.1695-1.4750.34591.06350.05710.0521.41670.29911.891713.029229.118437.273
21.64660.22070.24895.25355.70956.1357-1.43690.6705-0.03370.95670.2882.46070.1574-1.45851.47730.78160.0345-0.02341.49160.27751.508213.386140.719336.2915
33.4105-3.86921.17279.2657-2.15953.4971-0.05470.0806-0.00830.33570.19510.6781-0.1344-0.3285-0.18991.016-0.0239-0.08961.22690.10131.246516.225532.329837.3344
45.27263.118-1.2627.0806-2.90017.3741-0.11930.08860.5420.14640.20230.11110.5875-0.20410.04631.1430.0022-0.03511.2354-0.05761.208628.735711.219746.3502
56.09681.6806-0.366.6264-3.32684.4174-0.51160.29061.4104-0.48510.57190.42220.37310.5044-0.24471.37320.1245-0.06171.1901-0.21731.22226.869414.926240.7153
62.71582.1502-3.85437.0263-0.36716.79130.7736-0.47461.70641.1503-0.02951.1336-0.7413-0.3715-1.15371.365-0.02090.051.10850.07951.346532.801861.565527.9732
74.71713.1726-0.70546.4853-2.22914.41250.4904-0.01880.21260.2474-0.01730.1327-0.36170.0132-0.4160.96710.05680.14861.2053-0.06491.264931.407551.47928.3112
86.3212.29243.77093.4027-1.15559.34352.9189-1.25362.6344.27091.3657-1.1514-0.70192.0628-2.27682.2371-0.13010.1371.6964-0.31961.845239.668730.754927.2828
95.9832-1.3572-1.15022.78431.93922.79440.01060.6133-0.3005-1.01830.30030.10910.3003-0.1964-0.26471.144-0.0579-0.06831.10870.02390.99931.762842.62178.9606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'K' and (resid 25 through 51 )
2X-RAY DIFFRACTION2chain 'K' and (resid 52 through 73 )
3X-RAY DIFFRACTION3chain 'K' and (resid 74 through 134 )
4X-RAY DIFFRACTION4chain 'K' and (resid 135 through 201 )
5X-RAY DIFFRACTION5chain 'K' and (resid 202 through 223 )
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 25 )
7X-RAY DIFFRACTION7chain 'H' and (resid 26 through 123 )
8X-RAY DIFFRACTION8chain 'L' and (resid -7 through 3 )
9X-RAY DIFFRACTION9chain 'L' and (resid 4 through 108 )

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