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- PDB-9bl5: KIR3DL1*001 in complex with HLA-A*24:02 presenting the TW9 peptide -

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Basic information

Entry
Database: PDB / ID: 9bl5
TitleKIR3DL1*001 in complex with HLA-A*24:02 presenting the TW9 peptide
Components
  • Beta-2-microglobulin
  • Killer cell immunoglobulin-like receptor 3DL1
  • MHC class I antigen
  • Polymerase basic protein 2 peptide
KeywordsIMMUNE SYSTEM / immunoglobulin fold / natural killer cell receptor / Kir
Function / homology
Function and homology information


HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / natural killer cell mediated cytotoxicity / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / negative regulation of receptor binding / early endosome lumen ...HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / natural killer cell mediated cytotoxicity / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / 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 / 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 / virion component / 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 / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / molecular adaptor activity / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / symbiont-mediated suppression of host gene expression / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / DNA-templated transcription / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / PB2, C-terminal / : / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / Immunoglobulin / Immunoglobulin domain ...: / PB2, C-terminal / : / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / Immunoglobulin / Immunoglobulin domain / 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
MHC class I antigen / Killer cell immunoglobulin-like receptor 3DL1 / Beta-2-microglobulin / Polymerase basic protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
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

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Polymerase basic protein 2 peptide
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3086
Polymers79,8654
Non-polymers4422
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-19 kcal/mol
Surface area31430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.437, 62.119, 67.000
Angle α, β, γ (deg.)93.444, 100.673, 109.966
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 MHC class I antigen


Mass: 31778.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Details (production host): pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A411J078
#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 / CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / Natural killer- ...CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / Natural killer-associated transcript 3 / NKAT-3 / p70 natural killer cell receptor clones CL-2/CL-11 / p70 NK receptor CL-2/CL-11


Mass: 34927.266 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, CD158E, NKAT3, NKB1 / Details (production host): pHLSEC / Production host: Homo sapiens (human) / References: UniProt: P43629

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Protein/peptide / Sugars / Non-polymers , 3 types, 185 molecules C

#3: Protein/peptide Polymerase basic protein 2 peptide / RNA-directed RNA polymerase subunit P3


Mass: 1280.453 Da / Num. of mol.: 1 / Fragment: residues 549-557 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: Q809Q3
#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.: 2
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.: 182 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
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: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2→48.09 Å / Num. obs: 50901 / % possible obs: 97.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 41.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3 / Num. unique obs: 3706 / CC1/2: 0.926

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.88 Å / SU ML: 0.2635 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 29.9074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2312 2511 4.94 %
Rwork0.2105 48368 -
obs0.2115 50879 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.89 Å2
Refinement stepCycle: LAST / Resolution: 2→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 28 182 5358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075340
X-RAY DIFFRACTIONf_angle_d0.88237272
X-RAY DIFFRACTIONf_chiral_restr0.0541765
X-RAY DIFFRACTIONf_plane_restr0.0082950
X-RAY DIFFRACTIONf_dihedral_angle_d14.04031886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.35231340.3162644X-RAY DIFFRACTION96.59
2.04-2.080.31281520.29612667X-RAY DIFFRACTION97.17
2.08-2.130.27551230.28072682X-RAY DIFFRACTION97.03
2.13-2.170.2631450.26742680X-RAY DIFFRACTION97.15
2.17-2.230.31061390.27272688X-RAY DIFFRACTION97.48
2.23-2.290.29761250.26232761X-RAY DIFFRACTION97.73
2.29-2.360.37291370.2712665X-RAY DIFFRACTION97.46
2.36-2.430.30831300.27012693X-RAY DIFFRACTION97.88
2.43-2.520.27781470.25972706X-RAY DIFFRACTION97.71
2.52-2.620.31161320.25712716X-RAY DIFFRACTION98
2.62-2.740.26241450.25862706X-RAY DIFFRACTION97.84
2.74-2.880.3141090.27282719X-RAY DIFFRACTION97.72
2.88-3.060.26271420.25272669X-RAY DIFFRACTION96.73
3.06-3.30.2471310.2322666X-RAY DIFFRACTION96.22
3.3-3.630.20431610.21282666X-RAY DIFFRACTION97.52
3.63-4.160.18431890.17082660X-RAY DIFFRACTION97.7
4.16-5.240.18991260.14982721X-RAY DIFFRACTION98
5.24-35.880.20471440.17272659X-RAY DIFFRACTION96.52

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