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- PDB-6pa1: Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA... -

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Basic information

Entry
Database: PDB / ID: 6pa1
TitleKiller cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*07:02
Components
  • ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEU
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, Cw-7 alpha chain
  • Killer cell immunoglobulin-like receptor 2DL2
KeywordsIMMUNE SYSTEM / KIR receptor / HLA / innate immunity / NK cell / T cell
Function / homology
Function and homology information


TAP binding / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression ...TAP binding / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / PRC2 methylates histones and DNA / 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 / Defective pyroptosis / HDACs deacetylate histones / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / RNA Polymerase I Promoter Escape / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / negative regulation of forebrain neuron differentiation / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / B-WICH complex positively regulates rRNA expression / response to molecule of bacterial origin / HDMs demethylate histones / 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 / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / positive regulation of receptor-mediated endocytosis / HCMV Early Events / MHC class II protein complex / cellular response to nicotine / Transcriptional regulation of granulopoiesis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / structural constituent of chromatin / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 / nucleosome / Interferon alpha/beta signaling / sensory perception of smell / nucleosome assembly / 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 / chromatin organization / late endosome membrane / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / Senescence-Associated Secretory Phenotype (SASP) / protein refolding
Similarity search - Function
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 / Histone H3 signature 1. / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-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 / Histone H3 signature 1. / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / MHC classes I/II-like antigen recognition protein / Histone-fold / 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
HLA class I histocompatibility antigen, C alpha chain / Killer cell immunoglobulin-like receptor 2DL2 / Beta-2-microglobulin / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsMoradi, S. / Rossjohn, J. / Vivian, J.P.
CitationJournal: Nat Commun / Year: 2021
Title: Structural plasticity of KIR2DL2 and KIR2DL3 enables altered docking geometries atop HLA-C.
Authors: Moradi, S. / Stankovic, S. / O'Connor, G.M. / Pymm, P. / MacLachlan, B.J. / Faoro, C. / Retiere, C. / Sullivan, L.C. / Saunders, P.M. / Widjaja, J. / Cox-Livingstone, S. / Rossjohn, J. / ...Authors: Moradi, S. / Stankovic, S. / O'Connor, G.M. / Pymm, P. / MacLachlan, B.J. / Faoro, C. / Retiere, C. / Sullivan, L.C. / Saunders, P.M. / Widjaja, J. / Cox-Livingstone, S. / Rossjohn, J. / Brooks, A.G. / Vivian, J.P.
History
DepositionJun 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, Cw-7 alpha chain
B: Beta-2-microglobulin
C: ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEU
D: Killer cell immunoglobulin-like receptor 2DL2
E: HLA class I histocompatibility antigen, Cw-7 alpha chain
F: Beta-2-microglobulin
G: ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEU
H: Killer cell immunoglobulin-like receptor 2DL2


Theoretical massNumber of molelcules
Total (without water)134,2158
Polymers134,2158
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, Cw-7 alpha chain
B: Beta-2-microglobulin
C: ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEU
D: Killer cell immunoglobulin-like receptor 2DL2


Theoretical massNumber of molelcules
Total (without water)67,1074
Polymers67,1074
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-26 kcal/mol
Surface area27460 Å2
MethodPISA
2
E: HLA class I histocompatibility antigen, Cw-7 alpha chain
F: Beta-2-microglobulin
G: ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEU
H: Killer cell immunoglobulin-like receptor 2DL2


Theoretical massNumber of molelcules
Total (without water)67,1074
Polymers67,1074
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-24 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.565, 82.086, 104.887
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, Cw-7 alpha chain / MHC class I antigen Cw*7


Mass: 31787.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C, HLAC / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P10321
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEU


Mass: 1034.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS
#4: Protein Killer cell immunoglobulin-like receptor 2DL2 / CD158 antigen-like family member B1 / MHC class I NK cell receptor / Natural killer-associated ...CD158 antigen-like family member B1 / MHC class I NK cell receptor / Natural killer-associated transcript 6 / NKAT-6 / p58 natural killer cell receptor clone CL-43 / p58 NK receptor CL-43


Mass: 22406.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR2DL2, CD158B1, NKAT6 / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P43627

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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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium tartrate dibasic dihydrate and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 20697 / % possible obs: 97 % / Redundancy: 4 % / Net I/σ(I): 4.6
Reflection shellResolution: 3→3.12 Å / Redundancy: 3.8 % / Num. unique obs: 2015 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFX

1efx


Resolution: 3.01→32.321 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.45
RfactorNum. reflection% reflection
Rfree0.3096 1158 5.16 %
Rwork0.263 --
obs0.2655 22437 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.01→32.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9088 0 0 0 9088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029370
X-RAY DIFFRACTIONf_angle_d0.71112709
X-RAY DIFFRACTIONf_dihedral_angle_d12.0795604
X-RAY DIFFRACTIONf_chiral_restr0.0421311
X-RAY DIFFRACTIONf_plane_restr0.0041672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0096-3.14640.51441500.49162500X-RAY DIFFRACTION91
3.1464-3.31210.37021460.33112617X-RAY DIFFRACTION96
3.3121-3.51940.35421510.29082617X-RAY DIFFRACTION96
3.5194-3.79080.37181390.29722608X-RAY DIFFRACTION94
3.7908-4.17150.30391330.2782640X-RAY DIFFRACTION96
4.1715-4.77350.27751330.22922698X-RAY DIFFRACTION97
4.7735-6.00780.24281540.21782775X-RAY DIFFRACTION100
6.0078-32.32330.2651520.21252824X-RAY DIFFRACTION100
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)
11.5078-1.04391.6091.1235-1.02813.30090.0780.0358-0.00280.08820.03440.26360.1664-0.0379-0.09640.3348-0.07490.10340.3870.03110.4197-20.2797-21.3332-43.2299
26.3837-0.1620.1714.5979-0.67222.846-0.19930.01250.5754-0.00140.58580.6924-0.2077-0.5142-0.31880.55620.0649-0.02450.41540.09510.6026-30.3037-4.6929-42.306
30.4523-0.94270.28392.5549-0.04293.91651.05690.092-0.69920.03870.106-0.02130.04260.0802-0.79390.5704-0.00540.1006-0.0033-0.01060.6751-12.5718-28.3044-28.2498
43.4099-2.078-0.76782.66891.57161.4871-0.0473-0.07560.10890.1716-0.0003-0.1752-0.0410.04120.05730.3433-0.0886-0.04480.41980.05380.3599-2.8443-26.9338-5.3184
51.00150.5186-0.68530.695-0.33322.3198-0.0176-0.03960.053-0.01010.03990.2359-0.119-0.2183-0.04550.33880.0569-0.04810.40.02050.4177-20.464420.5696-9.0157
67.19280.75120.67134.4250.52162.0323-0.14970.0718-0.48070.0290.33040.9198-0.0251-0.1714-0.16130.46360.02120.08960.36090.08850.6238-30.46143.755-9.9452
71.81171.2137-1.0931.7706-1.57371.39530.48750.11850.19240.29920.1001-0.1741-0.32280.6295-0.43930.4113-0.0481-0.05640.4013-0.11810.4081-12.626427.4772-24.1855
84.25732.11150.5672.14280.951.3746-0.093-0.1346-0.1166-0.18940.0249-0.0201-0.1496-0.16660.06390.43310.14230.02090.33020.03860.3721-2.951325.9706-47.2659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 277)
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 98)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 9)
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 200)
5X-RAY DIFFRACTION5(chain 'E' and resid 2 through 277)
6X-RAY DIFFRACTION6(chain 'F' and resid 0 through 99)
7X-RAY DIFFRACTION7(chain 'G' and resid 1 through 9)
8X-RAY DIFFRACTION8(chain 'H' and resid 6 through 200)

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