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- PDB-9bl4: KIR3DL1*086 in complex with HLA-B*57:03 presenting the AW10 peptide -

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Basic information

Entry
Database: PDB / ID: 9bl4
TitleKIR3DL1*086 in complex with HLA-B*57:03 presenting the AW10 peptide
Components
  • Beta-2-microglobulin
  • Catenin alpha-1 peptide
  • HLA-B alpha chain (B*5703GB)
  • Killer cell immunoglobulin-like receptor 3DL1
KeywordsIMMUNE SYSTEM / immunoglobulin fold / natural killer cell receptor / Kir
Function / homology
Function and homology information


negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / Regulation of CDH11 function / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / cellular response to indole-3-methanol / vinculin binding ...negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / Regulation of CDH11 function / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / cellular response to indole-3-methanol / vinculin binding / flotillin complex / negative regulation of cell motility / apical junction assembly / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / catenin complex / Adherens junctions interactions / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of protein localization to nucleus / axon regeneration / negative regulation of neuroblast proliferation / smoothened signaling pathway / establishment or maintenance of cell polarity / Myogenesis / odontogenesis of dentin-containing tooth / intercalated disc / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / neuroblast proliferation / RHO GTPases activate IQGAPs / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / acrosomal vesicle / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / VEGFR2 mediated vascular permeability / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / integrin-mediated signaling pathway / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / adherens junction / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / cell-cell adhesion / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / beta-catenin binding / MHC class II protein complex / cellular response to nicotine / response to estrogen / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / male gonad development / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / actin filament binding / Modulation by Mtb of host immune system / positive regulation of T cell activation / cell-cell junction / sensory perception of smell / protein localization / cell migration / actin cytoskeleton / negative regulation of neuron projection development / positive regulation of protein binding / cell junction / tertiary granule lumen / DAP12 signaling / lamellipodium / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane
Similarity search - Function
Alpha-catenin / : / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal ...Alpha-catenin / : / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
HLA-B alpha chain (B*5703GB) / KIR3DL1 / Catenin alpha-1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFaoro, C. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2008981 Australia
CitationJournal: Cell / Year: 2024
Title: An archaic HLA class I receptor allele diversifies natural killer cell-driven immunity in First Nations peoples of Oceania.
Authors: Loh, L. / Saunders, P.M. / Faoro, C. / Font-Porterias, N. / Nemat-Gorgani, N. / Harrison, G.F. / Sadeeq, S. / Hensen, L. / Wong, S.C. / Widjaja, J. / Clemens, E.B. / Zhu, S. / Kichula, K.M. ...Authors: Loh, L. / Saunders, P.M. / Faoro, C. / Font-Porterias, N. / Nemat-Gorgani, N. / Harrison, G.F. / Sadeeq, S. / Hensen, L. / Wong, S.C. / Widjaja, J. / Clemens, E.B. / Zhu, S. / Kichula, K.M. / Tao, S. / Zhu, F. / Montero-Martin, G. / Fernandez-Vina, M. / Guethlein, L.A. / Vivian, J.P. / Davies, J. / Mentzer, A.J. / Oppenheimer, S.J. / Pomat, W. / Ioannidis, A.G. / Barberena-Jonas, C. / Moreno-Estrada, A. / Miller, A. / Parham, P. / Rossjohn, J. / Tong, S.Y.C. / Kedzierska, K. / Brooks, A.G. / Norman, P.J.
History
DepositionApr 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-B alpha chain (B*5703GB)
B: Beta-2-microglobulin
C: Catenin alpha-1 peptide
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2967
Polymers78,6324
Non-polymers6643
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-17 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.936, 60.537, 64.900
Angle α, β, γ (deg.)95.368, 96.497, 106.021
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 3 types, 3 molecules ABG

#1: Protein HLA-B alpha chain (B*5703GB) / MHC class I antigen / Human Leukocyte Antigen B*57:03


Mass: 31811.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Details (production host): pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3ZN84
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Details (production host): pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#4: Protein Killer cell immunoglobulin-like receptor 3DL1


Mass: 33884.242 Da / Num. of mol.: 1 / Fragment: residues 1-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1 / Details (production host): pHLSEC / Production host: Homo sapiens (human) / References: UniProt: I6LEK9

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Protein/peptide / Sugars / Non-polymers , 3 types, 458 molecules C

#3: Protein/peptide Catenin alpha-1 peptide / Alpha E-catenin / Cadherin-associated protein / Renal carcinoma antigen NY-REN-13


Mass: 1057.200 Da / Num. of mol.: 1 / Fragment: residues 850-859 (Uniprot numbering) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35221
#5: 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.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 16% PEG 3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953659 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953659 Å / Relative weight: 1
ReflectionResolution: 1.75→44.63 Å / Num. obs: 63547 / % possible obs: 93.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 24.34 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 8.9
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3559 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→44.63 Å / SU ML: 0.2271 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.8963 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 3169 4.99 %
Rwork0.1906 60352 -
obs0.1925 63521 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.14 Å2
Refinement stepCycle: LAST / Resolution: 1.75→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5189 0 42 454 5685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00685432
X-RAY DIFFRACTIONf_angle_d0.98297414
X-RAY DIFFRACTIONf_chiral_restr0.0619782
X-RAY DIFFRACTIONf_plane_restr0.0064968
X-RAY DIFFRACTIONf_dihedral_angle_d14.0311961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.31311300.28062640X-RAY DIFFRACTION94.41
1.78-1.80.32381400.27422736X-RAY DIFFRACTION94.67
1.8-1.830.31141330.25842635X-RAY DIFFRACTION94.6
1.83-1.870.2831420.25032651X-RAY DIFFRACTION94.2
1.87-1.90.28671510.25792638X-RAY DIFFRACTION94.35
1.9-1.940.27191640.23262640X-RAY DIFFRACTION94.32
1.94-1.980.22681270.21942663X-RAY DIFFRACTION93.94
1.98-2.020.24931450.21342623X-RAY DIFFRACTION93.74
2.02-2.060.24711110.21182654X-RAY DIFFRACTION93.51
2.06-2.120.23761500.19822661X-RAY DIFFRACTION93.73
2.12-2.170.23711320.20232646X-RAY DIFFRACTION94.46
2.17-2.240.26671350.20032677X-RAY DIFFRACTION94.11
2.24-2.310.22881290.1982618X-RAY DIFFRACTION93.06
2.31-2.390.29791390.20752642X-RAY DIFFRACTION93.79
2.39-2.490.25741250.21892624X-RAY DIFFRACTION92.22
2.49-2.60.28821510.22072590X-RAY DIFFRACTION91.46
2.6-2.740.26631310.21542564X-RAY DIFFRACTION91.76
2.74-2.910.2511260.20332573X-RAY DIFFRACTION90.45
2.91-3.130.22981520.18982514X-RAY DIFFRACTION90.5
3.13-3.450.22431360.17682569X-RAY DIFFRACTION91.23
3.45-3.950.17731470.15982558X-RAY DIFFRACTION91.63
3.95-4.970.17871300.13942626X-RAY DIFFRACTION92.7

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