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- PDB-7duu: Crystal structure of HLA molecule with an KIR receptor -

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Basic information

Entry
Database: PDB / ID: 7duu
TitleCrystal structure of HLA molecule with an KIR receptor
Components
  • Beta-2-microglobulin
  • Killer cell immunoglobulin-like receptor 2DS2
  • LEU-ASN-PRO-SER-VAL-ALA-ALA-THR-LEU
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA
Function / homology
Function and homology information


stimulatory killer cell immunoglobulin-like receptor signaling pathway / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway ...stimulatory killer cell immunoglobulin-like receptor signaling pathway / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / transmembrane signaling receptor activity / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / ER-Phagosome pathway / iron ion transport / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 / Immunoglobulin subtype ...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 / Immunoglobulin subtype / Immunoglobulin / 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
MHC class I antigen / Killer cell immunoglobulin-like receptor 2DS2 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepacivirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsYang, Y. / Yin, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Immunology / Year: 2022
Title: Activating receptor KIR2DS2 bound to HLA-C1 reveals the novel recognition features of activating receptor.
Authors: Yang, Y. / Bai, H. / Wu, Y. / Chen, P. / Zhou, J. / Lei, J. / Ye, X. / Brown, A.J. / Zhou, X. / Shu, T. / Chen, Y. / Wei, P. / Yin, L.
History
DepositionJan 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: LEU-ASN-PRO-SER-VAL-ALA-ALA-THR-LEU
D: Killer cell immunoglobulin-like receptor 2DS2


Theoretical massNumber of molelcules
Total (without water)66,5834
Polymers66,5834
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-25 kcal/mol
Surface area28110 Å2
Unit cell
Length a, b, c (Å)82.056, 153.962, 177.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

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Components

#1: Protein MHC class I antigen / HLA


Mass: 31769.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: F6IQA6
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P61769
#3: Protein/peptide LEU-ASN-PRO-SER-VAL-ALA-ALA-THR-LEU


Mass: 885.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Production host: Escherichia coli K-12 (bacteria)
#4: Protein Killer cell immunoglobulin-like receptor 2DS2 / CD158 antigen-like family member J / MHC class I NK cell receptor / NK receptor 183 ActI / Natural ...CD158 antigen-like family member J / MHC class I NK cell receptor / NK receptor 183 ActI / Natural killer-associated transcript 5 / NKAT-5 / p58 natural killer cell receptor clone CL-49 / p58 NK receptor CL-49


Mass: 22048.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR2DS2, CD158J, NKAT5 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P43631
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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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: 4.21 Å3/Da / Density % sol: 70.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 87 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.51→44.39 Å / Num. obs: 38710 / % possible obs: 99 % / Redundancy: 6.3 % / Biso Wilson estimate: 46.98 Å2 / CC1/2: 0.961 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.83
Reflection shellResolution: 2.51→2.6 Å / Rmerge(I) obs: 0.561 / Num. unique obs: 3797 / CC1/2: 0.867

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M4K ,4NT6

1m4k

4nt6


Resolution: 2.51→44.39 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 1997 5.16 %
Rwork0.2003 36709 -
obs0.2027 38706 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.84 Å2 / Biso mean: 56.0402 Å2 / Biso min: 22.43 Å2
Refinement stepCycle: final / Resolution: 2.51→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 0 127 4791
Biso mean---51.36 -
Num. residues----578
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.51-2.570.29731380.25622526266497
2.57-2.640.25671400.2322582272299
2.64-2.720.26291400.22062578271899
2.72-2.80.25041380.23072558269699
2.8-2.90.27661430.236226132756100
2.9-3.020.2931420.225726162758100
3.02-3.160.31291430.226326252768100
3.16-3.320.30261410.220726062747100
3.32-3.530.2581440.211326482792100
3.53-3.810.23351430.192326252768100
3.81-4.190.23211440.180226432787100
4.19-4.790.20831460.161626722818100
4.79-6.040.23331450.189226862831100
6.04-44.390.21661500.19932731288197
Refinement TLS params.Method: refined / Origin x: -38.309 Å / Origin y: -53.6489 Å / Origin z: -20.0788 Å
111213212223313233
T0.3279 Å2-0.0156 Å20.0156 Å2-0.2251 Å20.0532 Å2--0.2939 Å2
L1.5188 °2-0.1826 °20.42 °2-0.6894 °2-0.1174 °2--1.7456 °2
S-0.0121 Å °-0.1223 Å °0.0226 Å °-0.1643 Å °0.0294 Å °-0.0237 Å °-0.114 Å °-0.0038 Å °-0.0169 Å °
Refinement TLS groupSelection details: all

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