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- PDB-9bl3: KIR3DL1*114 in complex with HLA-B*57:03 presenting the AW10 peptide -

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Basic information

Entry
Database: PDB / ID: 9bl3
TitleKIR3DL1*114 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 / flotillin complex ...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 / flotillin complex / vinculin binding / catenin complex / apical junction assembly / negative regulation of cell motility / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / Adherens junctions interactions / negative regulation of protein localization to nucleus / axon regeneration / negative regulation of neuroblast proliferation / smoothened signaling pathway / Myogenesis / establishment or maintenance of cell polarity / odontogenesis of dentin-containing tooth / antigen processing and presentation of peptide antigen via MHC class I / intercalated disc / neuroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / RHO GTPases activate IQGAPs / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / acrosomal vesicle / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / VEGFR2 mediated vascular permeability / cellular response to iron ion / integrin-mediated signaling pathway / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / adherens junction / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cell-cell adhesion / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / beta-catenin binding / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / response to estrogen / male gonad development / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / actin filament binding / Modulation by Mtb of host immune system / cell-cell junction / late endosome membrane / cell junction / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / intracellular protein localization / DAP12 signaling / cell migration / T cell differentiation in thymus / lamellipodium / actin cytoskeleton / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation
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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
Killer cell immunoglobulin-like receptor 3DL1 / HLA-B alpha chain (B*5703GB) / Catenin alpha-1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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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)79,5328
Polymers78,6474
Non-polymers8854
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-14 kcal/mol
Surface area32350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.769, 60.784, 65.042
Angle α, β, γ (deg.)95.564, 98.163, 109.016
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: 33899.281 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 / Production host: Homo sapiens (human) / References: UniProt: A0A5J6VN80

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Protein/peptide / Sugars / Non-polymers , 3 types, 390 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.: 4
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.: 385 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
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 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953659 Å / Relative weight: 1
ReflectionResolution: 2→48.1 Å / Num. obs: 48382 / % possible obs: 97.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 37.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.9
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3548 / CC1/2: 0.85 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.1 Å / SU ML: 0.2566 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.9019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2289 2351 4.86 %
Rwork0.193 46018 -
obs0.1947 48369 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.05 Å2
Refinement stepCycle: LAST / Resolution: 2→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5334 0 56 385 5775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00735592
X-RAY DIFFRACTIONf_angle_d0.89577625
X-RAY DIFFRACTIONf_chiral_restr0.0548807
X-RAY DIFFRACTIONf_plane_restr0.0077997
X-RAY DIFFRACTIONf_dihedral_angle_d14.12892032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.32821240.30032688X-RAY DIFFRACTION96.77
2.04-2.090.31061430.26972681X-RAY DIFFRACTION97.21
2.09-2.130.29821370.26022702X-RAY DIFFRACTION97.09
2.13-2.190.27711640.24422667X-RAY DIFFRACTION96.92
2.19-2.250.29591310.23972708X-RAY DIFFRACTION97.39
2.25-2.310.2671380.23332684X-RAY DIFFRACTION97.82
2.31-2.390.24911300.23282715X-RAY DIFFRACTION97.46
2.39-2.470.26581450.23382739X-RAY DIFFRACTION97.7
2.47-2.570.27921310.24012706X-RAY DIFFRACTION97.63
2.57-2.690.31981310.23552689X-RAY DIFFRACTION97.85
2.69-2.830.29681360.23372727X-RAY DIFFRACTION97.38
2.83-3.010.26141360.22922721X-RAY DIFFRACTION98.14
3.01-3.240.24261450.21272737X-RAY DIFFRACTION98.19
3.24-3.570.19511480.18592674X-RAY DIFFRACTION97.85
3.57-4.080.19671290.15942765X-RAY DIFFRACTION98.2
4.08-5.140.18281470.13682684X-RAY DIFFRACTION97.52
5.14-48.10.19541360.16272731X-RAY DIFFRACTION98.49

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