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

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Basic information

Entry
Database: PDB / ID: 9lrf
TitleKiller immunoglobulin receptor KIR2DL2 in complex with KIR2DL2_KIR2DL2/3 agonist 61-Fab
Components
  • KIR2DL2_KIR2DL2/3 agonist 61 FAB FRAGMENT HEAVY CHAIN
  • KIR2DL2_KIR2DL2/3 agonist 61 FAB FRAGMENT LIGHT CHAIN
  • 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: 2.5 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 FAB FRAGMENT HEAVY CHAIN
L: KIR2DL2_KIR2DL2/3 agonist 61 FAB FRAGMENT LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8075
Polymers70,3653
Non-polymers4422
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-17 kcal/mol
Surface area29700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.109, 79.244, 64.364
Angle α, β, γ (deg.)90.00, 92.39, 90.00
Int Tables number5
Space group name H-MC121

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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 FAB FRAGMENT HEAVY CHAIN


Mass: 24105.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody KIR2DL2_KIR2DL2/3 agonist 61 FAB FRAGMENT LIGHT CHAIN


Mass: 23024.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: 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: obtained synthetically / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 100mM imidazole-HCl pH7.5, 200mM Calcium acetate, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→48.33 Å / Num. obs: 29367 / % possible obs: 98.9 % / Redundancy: 3.4 % / CC1/2: 0.982 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.044 / Rrim(I) all: 0.082 / Χ2: 0.79 / Net I/σ(I): 8.9 / Num. measured all: 99820
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 1.085 / Num. measured all: 11977 / Num. unique obs: 3339 / CC1/2: 0.551 / Rpim(I) all: 0.662 / Rrim(I) all: 1.273 / Χ2: 0.53 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DL2

2dl2


Resolution: 2.5→38.08 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 1454 4.95 %
Rwork0.2338 --
obs0.2358 29353 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 0 28 14 4674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024776
X-RAY DIFFRACTIONf_angle_d0.5246510
X-RAY DIFFRACTIONf_dihedral_angle_d15.641662
X-RAY DIFFRACTIONf_chiral_restr0.043738
X-RAY DIFFRACTIONf_plane_restr0.005836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.39481370.38412805X-RAY DIFFRACTION99
2.59-2.690.41411410.3482810X-RAY DIFFRACTION99
2.69-2.820.3371430.33212772X-RAY DIFFRACTION99
2.82-2.960.37371360.32982799X-RAY DIFFRACTION99
2.96-3.150.38711370.30182808X-RAY DIFFRACTION99
3.15-3.390.34541650.28062782X-RAY DIFFRACTION99
3.39-3.730.28621420.26192752X-RAY DIFFRACTION98
3.73-4.270.2551460.21142781X-RAY DIFFRACTION98
4.27-5.380.19891600.17022747X-RAY DIFFRACTION97
5.38-38.080.25351470.20682843X-RAY DIFFRACTION98
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)
13.31510.83450.0383.3535-1.39421.70940.02120.07841.0421-0.0163-0.3232-0.4912-0.49930.09020.05810.73760.04380.0920.56540.03491.146349.820654.3333-3.8523
21.046-0.3684-0.38140.42960.34072.83110.2790.29951.2528-0.44460.0464-0.6684-0.31150.50360.06820.68450.09330.10350.70610.16651.32651.617853.6665-5.0903
31.5039-2.097-2.6759.25051.1975.75170.50330.9472.27130.7352-0.0411-1.73510.10651.53230.16430.82150.00460.02510.9127-0.11291.300953.485560.33245.623
43.3980.96781.45441.4953-0.45571.1623-0.031-0.0170.2135-0.8016-0.0895-0.22640.2131-0.2019-0.10810.88760.0746-0.14030.8243-0.00990.764927.356742.4246-16.0651
52.3508-1.07570.33291.5836-1.59973.52890.04830.5943-0.7789-1.3245-1.1280.1198-0.1222-0.497-0.11490.8862-0.0547-0.13881.2013-0.16131.061223.912939.9203-10.6742
62.81980.89640.40422.6553-0.63732.08460.02780.49520.0055-0.6412-0.22340.20020.15390.33770.10440.82420.1152-0.0660.7343-0.02160.665328.469544.5934-15.6521
73.9451-2.1357-0.16622.8447-0.76374.5464-0.2205-0.63860.8511.08170.24390.0975-0.198-0.2214-0.07870.78250.0283-0.06030.6799-0.17710.674155.701536.652816.3431
81.5527-0.61310.28393.187-2.20961.7493-0.2177-0.40080.37070.98140.1911-0.3262-0.6323-0.60920.06620.80420.0537-0.05270.7732-0.15990.736957.475832.281817.4362
92.80480.6914-0.19662.86261.72653.6092-0.29660.2301-0.0929-0.16280.21120.1109-0.0692-0.37460.04870.5814-0.0328-0.06280.7341-0.08730.711364.52992.752451.7679
104.2-0.63810.20746.0408-0.55461.60560.07750.3170.0957-0.364-0.0186-0.82440.04970.2816-0.03260.4312-0.00910.02010.4988-0.05660.549465.337222.77110.6269
114.04950.52730.11494.5051-0.88783.5507-0.2963-0.5546-0.49570.55850.11560.18460.40470.09240.25410.6940.15140.14740.80180.13010.812790.576-5.723419.6161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'K' and (resid 25 through 73 )
2X-RAY DIFFRACTION2chain 'K' and (resid 74 through 103 )
3X-RAY DIFFRACTION3chain 'K' and (resid 104 through 117 )
4X-RAY DIFFRACTION4chain 'K' and (resid 118 through 162 )
5X-RAY DIFFRACTION5chain 'K' and (resid 163 through 180 )
6X-RAY DIFFRACTION6chain 'K' and (resid 181 through 221 )
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 73 )
8X-RAY DIFFRACTION8chain 'H' and (resid 74 through 129 )
9X-RAY DIFFRACTION9chain 'H' and (resid 130 through 224 )
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 111 )
11X-RAY DIFFRACTION11chain 'L' and (resid 112 through 210 )

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