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- PDB-6pag: Killer cell immunoglobulin-like receptor 2DL3 in complex with HLA... -

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Basic information

Entry
Database: PDB / ID: 6pag
TitleKiller cell immunoglobulin-like receptor 2DL3 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 2DL3
KeywordsIMMUNE SYSTEM / KIR receptor / HLA / innate immunity / NK cell / T cell
Function / homology
Function and homology information


immune response-regulating signaling pathway / TAP binding / 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 / antigen binding / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication ...immune response-regulating signaling pathway / TAP binding / 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 / antigen binding / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression / DAP12 interactions / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / transferrin transport / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / cellular response to iron ion / PRC2 methylates histones and DNA / Endosomal/Vacuolar pathway / Regulation of endogenous retroelements by KRAB-ZFP proteins / lumenal side of endoplasmic reticulum membrane / Defective pyroptosis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HDACs deacetylate histones / peptide antigen assembly with MHC class II protein complex / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / 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 / Transcriptional regulation by small RNAs / 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 / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / 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 / NoRC negatively regulates rRNA expression / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / B-WICH complex positively regulates rRNA expression / cellular response to nicotine / PKMTs methylate histone lysines / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / Meiotic recombination / Pre-NOTCH Transcription and Translation / specific granule lumen / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / phagocytic vesicle membrane / recycling endosome membrane / Transcriptional regulation of granulopoiesis / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / HCMV Early Events / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / structural constituent of chromatin / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / nucleosome / T cell differentiation in thymus / nucleosome assembly / signaling receptor activity / negative regulation of neuron projection development / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / 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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like ...: / 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 / Histone H3 signature 1. / : / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, C alpha chain / Killer cell immunoglobulin-like receptor 2DL3 / Beta-2-microglobulin / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 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 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 2DL3


Theoretical massNumber of molelcules
Total (without water)67,1754
Polymers67,1754
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-22 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.855, 111.855, 87.994
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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


Mass: 31874.961 Da / Num. of mol.: 1
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.: 1
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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS
#4: Protein Killer cell immunoglobulin-like receptor 2DL3 / CD158 antigen-like family member B2 / KIR-023GB / Killer inhibitory receptor cl 2-3 / MHC class I ...CD158 antigen-like family member B2 / KIR-023GB / Killer inhibitory receptor cl 2-3 / MHC class I NK cell receptor / NKAT2a / NKAT2b / Natural killer-associated transcript 2 / NKAT-2 / p58 natural killer cell receptor clone CL-6 / p58 NK receptor CL-6 / p58.2 MHC class-I-specific NK receptor


Mass: 22386.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR2DL3, CD158B2, KIRCL23, NKAT2 / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P43628
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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Ammonium acetate, 0.1 M Tris-HCl pH.8.0 and 25% 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 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 21403 / % possible obs: 98.5 % / Redundancy: 3.1 % / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 2136 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFX

1efx


Resolution: 2.501→32.567 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.12
RfactorNum. reflection% reflection
Rfree0.2541 1097 5.13 %
Rwork0.2226 --
obs0.2242 21400 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→32.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4469 0 0 0 4469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0464602
X-RAY DIFFRACTIONf_angle_d1.6916229
X-RAY DIFFRACTIONf_dihedral_angle_d19.5141713
X-RAY DIFFRACTIONf_chiral_restr0.097638
X-RAY DIFFRACTIONf_plane_restr0.006824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5012-2.6150.3731390.34792518X-RAY DIFFRACTION99
2.615-2.75280.35171400.32842541X-RAY DIFFRACTION99
2.7528-2.92520.33291360.31262536X-RAY DIFFRACTION99
2.9252-3.15090.35251330.28722559X-RAY DIFFRACTION99
3.1509-3.46760.29131460.24542532X-RAY DIFFRACTION99
3.4676-3.96870.22551350.2122532X-RAY DIFFRACTION99
3.9687-4.99720.21611370.17672523X-RAY DIFFRACTION98
4.9972-32.56940.21791310.19412562X-RAY DIFFRACTION97
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)
10.53830.1036-0.23361.80690.39272.5256-0.14360.05250.0343-0.070.2191-0.11920.1940.123300.4278-0.01580.04340.4755-0.04470.51724.730724.21330.5787
20.9624-0.36280.87681.42740.70462.4436-0.35210.24520.0983-0.18280.16220.52820.0391-0.4331-0.47270.4972-0.1002-0.0210.550.05390.526116.78436.2746-11.5004
30.040.19620.45380.96310.09650.60060.02230.27090.025-0.2218-0.11160.29950.41420.06630.00120.6337-0.10190.02660.5769-0.12070.647812.008913.993-0.9741
40.13841.4396-0.34040.7709-0.04272.3052-0.01640.10970.21240.3116-0.21120.4261-0.0037-0.556400.58740.06330.12020.6564-0.0680.66323.946425.361830.7639
50.00360.0256-0.02080.02130.00820.01870.41970.2321.2663-0.0202-0.2493-0.0385-0.6977-0.39250.00010.9682-0.040.10030.8142-0.06461.008123.527740.336913.5049
60.01440.0258-0.01530.03130.00990.01680.0055-0.6444-0.5658-0.39550.17330.10090.0731-0.8654-00.61510.106-0.07830.5928-0.01380.560419.949426.847626.4713
7-0.0165-0.0029-0.008-0.01130.02730.03970.3834-0.3247-0.45550.1312-0.0184-0.07090.17820.548500.91280.0187-0.17640.84010.04690.809419.617812.544534.2079
8-0.04790.01230.00320.0210.02460.06140.01380.00150.09360.04350.0603-0.1641-0.2624-0.117600.52840.00680.01360.6969-0.05120.551322.854724.090423.1911
90.0451-0.18970.0445-0.0739-0.22630.1521-0.0538-0.46360.96510.1136-0.3296-0.4665-0.42971.4667-0.00520.5366-0.0274-0.03590.93930.06820.54930.856629.889321.214
100.1980.09410.010.0308-0.01360.1758-0.1151-0.64530.39190.60840.2989-0.3609-0.52960.248-00.66880.1496-0.13581.3643-0.00461.154834.597821.499527.6709
110.15450.05220.0866-0.00170.02490.0416-0.1034-0.07010.17570.66210.04850.7341-0.5987-0.1491-00.48370.04370.01750.5078-0.03060.557920.289428.58229.4799
120.3780.3346-0.16550.3156-0.2540.1297-0.0765-0.0150.1640.1809-0.33550.3433-0.14371.0217-00.58650.08230.04160.72330.04430.556926.186220.337229.0427
13-0.0514-0.01110.00480.0447-0.06450.0383-0.55110.19390.87760.4524-0.0838-0.56710.18610.4009-0.00011.0293-0.0408-0.18351.22350.04380.92129.899529.084428.6893
140.0036-0.01920.0106-0.0040.01160.02160.1233-0.53680.25390.3101-0.6641.0085-0.86350.000600.8667-0.3512-0.05321.1792-0.08120.626230.100240.018422.3321
150.0009-0.02540.04560.0670.00030.116-0.5508-0.7471-0.15420.54130.32470.50890.96540.243900.76790.02920.06150.9071-0.05350.700421.545127.484134.2185
160.0190.1708-0.09270.4609-0.14350.28560.5844-0.3828-0.47370.9359-0.89210.41910.5274-0.1917-0.00050.48220.0136-0.04480.7087-0.06940.754123.678923.6613-7.8122
170.40940.0521-0.86230.3138-0.12212.566-0.37210.1124-0.0047-0.18240.0435-0.21530.54970.034900.8078-0.14630.21320.7997-0.08140.910950.540130.6072-18.5988
180.3329-0.5439-0.02830.2305-0.19660.6306-0.32160.38360.3239-0.41780.09020.13590.0549-0.329-0.00451.0025-0.44040.04981.20520.01050.671428.369639.289-29.996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 126 )
2X-RAY DIFFRACTION2chain 'A' and (resid 127 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 185 )
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 278 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 5 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 11 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 20 )
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 30 )
9X-RAY DIFFRACTION9chain 'B' and (resid 31 through 41 )
10X-RAY DIFFRACTION10chain 'B' and (resid 42 through 51 )
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 61 )
12X-RAY DIFFRACTION12chain 'B' and (resid 62 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 83 )
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 99 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 9 )
17X-RAY DIFFRACTION17chain 'D' and (resid 5 through 110 )
18X-RAY DIFFRACTION18chain 'D' and (resid 111 through 195 )

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