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- PDB-7k81: KIR3DL1*005 in complex with HLA-A*24:02 presenting the RYPLTFGW p... -

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Open data


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Basic information

Entry
Database: PDB / ID: 7k81
TitleKIR3DL1*005 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide
Components
  • ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP
  • Beta-2-microglobulin
  • KIR3DL1
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / KIR receptor / HLA / peptide presentation
Function / homology
Function and homology information


: / Nef mediated downregulation of CD28 cell surface expression / HLA-B specific inhibitory MHC class I receptor activity / Late Phase of HIV Life Cycle / Nef Mediated CD8 Down-regulation / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / natural killer cell mediated cytotoxicity / Nef Mediated CD4 Down-regulation ...: / Nef mediated downregulation of CD28 cell surface expression / HLA-B specific inhibitory MHC class I receptor activity / Late Phase of HIV Life Cycle / Nef Mediated CD8 Down-regulation / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / natural killer cell mediated cytotoxicity / Nef Mediated CD4 Down-regulation / Nef and signal transduction / Uncoating of the HIV Virion / host cell Golgi membrane / antigen processing and presentation / Binding and entry of HIV virion / 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 / virion component / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Assembly Of The HIV Virion / 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 / Budding and maturation of HIV virion / 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 / SH3 domain binding / 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 / 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 / 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 / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / molecular adaptor activity / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / signaling receptor binding / virus-mediated perturbation of host defense response / Neutrophil degranulation / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space
Similarity search - Function
HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 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 ...HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 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
MHC class I antigen / MHC class I antigen / KIR3DL1 / Protein Nef / Killer cell immunoglobulin-like receptor 3DL1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMacLachlan, B.J. / Rossjohn, J. / Vivian, J.P.
CitationJournal: J Immunol. / Year: 2021
Title: The Role of the HLA Class I alpha 2 Helix in Determining Ligand Hierarchy for the Killer Cell Ig-like Receptor 3DL1.
Authors: Saunders, P.M. / MacLachlan, B.J. / Widjaja, J. / Wong, S.C. / Oates, C.V.L. / Rossjohn, J. / Vivian, J.P. / Brooks, A.G.
History
DepositionSep 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 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: MHC class I antigen
B: Beta-2-microglobulin
C: ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP
G: KIR3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6088
Polymers76,7234
Non-polymers8854
Water4,684260
1
G: KIR3DL1
hetero molecules

A: MHC class I antigen
B: Beta-2-microglobulin
C: ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP


Theoretical massNumber of molelcules
Total (without water)77,6088
Polymers76,7234
Non-polymers8854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area6850 Å2
ΔGint-4 kcal/mol
Surface area33020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.807, 61.385, 66.989
Angle α, β, γ (deg.)94.32, 99.82, 105.97
Int Tables number1
Space group name H-MP1

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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 / Plasmid: pET-30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A411J078, UniProt: A0A5H2UYS3*PLUS
#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: pET-30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61769
#4: Protein KIR3DL1


Mass: 32025.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: I6LEL9, UniProt: P43629*PLUS

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Protein/peptide / Sugars / Non-polymers , 3 types, 265 molecules C

#3: Protein/peptide ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP


Mass: 1040.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P04601*PLUS
#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.: 260 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 48.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 14% PEG 3350, 2% tacsimate, pH 5.0, and 0.1 M trisodium 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: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→34.02 Å / Num. obs: 46315 / % possible obs: 96 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 25532 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VH8

3vh8


Resolution: 2→34.02 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 2343 5.06 %
Rwork0.1901 --
obs0.1928 46315 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5322 0 56 260 5638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035542
X-RAY DIFFRACTIONf_angle_d0.737522
X-RAY DIFFRACTIONf_dihedral_angle_d10.936764
X-RAY DIFFRACTIONf_chiral_restr0.045787
X-RAY DIFFRACTIONf_plane_restr0.005979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.31221330.29792565X-RAY DIFFRACTION95
2.04-2.090.34871300.27742606X-RAY DIFFRACTION95
2.09-2.130.3111270.26592538X-RAY DIFFRACTION95
2.13-2.190.27621280.25192604X-RAY DIFFRACTION95
2.19-2.250.29361360.24782559X-RAY DIFFRACTION95
2.25-2.310.30151420.23912550X-RAY DIFFRACTION95
2.31-2.390.28821360.23392624X-RAY DIFFRACTION96
2.39-2.470.31241500.22522570X-RAY DIFFRACTION96
2.47-2.570.29881490.23262582X-RAY DIFFRACTION96
2.57-2.690.26491490.21322591X-RAY DIFFRACTION96
2.69-2.830.2741400.21832581X-RAY DIFFRACTION96
2.83-3.010.26021250.21392616X-RAY DIFFRACTION96
3.01-3.240.25751310.20192619X-RAY DIFFRACTION97
3.24-3.560.2371160.1722619X-RAY DIFFRACTION97
3.56-4.080.19961560.15142610X-RAY DIFFRACTION97
4.08-5.140.18711250.12832640X-RAY DIFFRACTION97
5.14-34.020.19521700.15322498X-RAY DIFFRACTION94
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)
12.9637-2.0445-0.4055.77821.18473.60470.2081-0.0581-0.0004-0.35370.1192-0.5460.25170.1713-0.25520.24170.0019-0.02780.1628-0.02120.19165.38726.026-9.3563
29.5824-5.2914-4.82735.21823.57015.540.28330.06610.0753-0.72290.0198-0.0129-0.0571-0.2096-0.29340.2668-0.0269-0.05520.16950.03430.1501-0.715613.8145-16.0441
32.7253-1.3260.30764.60991.92453.60840.0768-0.0791-0.3523-0.08460.43570.53180.4571-0.55310.10890.2937-0.1004-0.1170.31580.07590.2862-8.95496.2054-8.817
42.0025-0.22821.09050.57410.93273.26690.4227-0.2914-0.5301-0.20450.22830.29850.5917-1.3090.10380.2995-0.1898-0.20830.49310.1280.451-16.53787.2927-15.2228
51.6691-0.07730.052.46270.43214.8570.1612-0.0709-0.2366-0.1729-0.02750.05460.88040.1821-0.16810.4361-0.0237-0.10070.1044-0.04040.4314.2723-13.09430.4067
61.6435-0.62340.48172.5008-0.94983.32250.0528-0.1669-0.34390.01870.2740.54930.8463-0.7231-0.11190.4807-0.1634-0.10490.27910.11830.4314-1.5622-16.627414.8909
73.53270.78384.19238.86541.49185.06470.55330.630.9903-1.0386-0.21011.3215-0.0747-1.32110.28980.19380.04710.05840.79620.12570.3815-7.891412.27618.5732
86.5325-5.03441.0947.83243.2794.43060.49910.168-0.0077-0.6930.3168-0.19780.117-0.3919-0.63460.09550.0021-0.0140.23030.12090.16025.1447-0.47213.1428
92.61840.40750.93480.0660.15560.32430.58220.3163-1.80.4867-0.1645-1.06240.95110.9426-0.26890.6630.2849-0.34190.3681-0.14240.776818.2939-9.215914.0502
104.7873-1.67162.67915.1469-1.01996.02130.3141-0.218-0.69350.17720.1436-0.00850.50060.0615-0.30710.1355-0.02150.00240.1828-0.0480.17098.65420.90019.2989
115.6636-2.71675.14692.7873-2.32516.5768-0.32390.14590.37670.15210.0713-0.2701-0.99140.1782-0.04130.1890.07020.07510.3463-0.03140.19966.560311.24139.8693
120.92621.0556-1.61775.20540.89824.6504-0.13680.21250.2012-0.42050.3677-0.8579-1.35312.3573-0.32980.3054-0.03820.03620.5037-0.0510.338317.61659.042911.383
136.996-6.3327-0.31835.7682-0.18164.77940.5112-0.53-0.3434-0.3057-0.12050.2580.6391-0.4469-0.2970.2294-0.068-0.00310.29920.03240.1841-2.93974.6654-0.803
143.7584-1.89913.16566.3814-1.68524.02440.3598-0.0936-0.7422-0.07870.099-0.56330.2290.09780.24120.1944-0.02230.03460.2345-0.0150.256911.15492.6436.973
156.4989-0.1237-0.3328.4955-3.29331.63060.3687-2.2103-1.1032.57930.0178-1.28210.90980.6650.04420.74410.1547-0.27780.88690.02210.59220.0859-1.446623.6484
161.449-0.06550.48031.31460.76871.31270.1643-0.6042-0.26710.26970.00010.2946-0.1136-0.59930.25580.12260.12310.12580.4131-0.07270.14224.660512.26815.7507
175.5232-3.9821.39365.5621-2.54947.66480.3941-1.3153-0.88140.5175-0.21370.50270.7641-0.4501-0.28040.3485-0.0705-0.08330.34360.05330.31838.658-0.714220.2508
184.9887-5.697-0.19059.39370.70312.75470.5550.1754-0.572-0.9332-0.36570.17010.3336-0.7093-0.24770.4382-0.1599-0.13570.1990.04240.3862-5.37868.841-17.5537
196.49781.13352.44824.7393-0.92125.15810.4069-0.6016-0.24710.4258-0.3319-0.2803-0.38720.0051-0.07310.3867-0.0636-0.00570.197-0.04090.319111.928937.04341.4012
203.7905-0.19530.29550.4654-0.60562.3381-0.11190.62040.08370.12260.1948-0.223-0.50360.0921-0.08350.31290.01850.02930.25940.01470.22680.153336.5899-26.3364
217.31411.3324-0.87516.6016-0.86925.57330.12940.42350.1793-0.12160.016-0.6627-0.40120.4807-0.10380.22790.02740.06180.3321-0.03190.28265.138436.0138-25.8584
224.32652.16893.01151.79360.62592.71330.01270.11170.06030.1135-0.0478-0.0335-0.2888-0.057-0.03720.22950.06540.12060.2689-0.04850.2244-9.014232.5978-25.7636
235.4428-0.20510.93323.19650.32954.48540.3083-0.26350.1044-0.04420.07280.2787-0.2375-0.1719-0.35990.17270.01380.09270.3161-0.01130.2349-24.934225.6044-30.0116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 276 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 5 )
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 11 )
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 19 )
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 30 )
11X-RAY DIFFRACTION11chain 'B' and (resid 31 through 41 )
12X-RAY DIFFRACTION12chain 'B' and (resid 42 through 51 )
13X-RAY DIFFRACTION13chain 'B' and (resid 52 through 61 )
14X-RAY DIFFRACTION14chain 'B' and (resid 62 through 71 )
15X-RAY DIFFRACTION15chain 'B' and (resid 72 through 77 )
16X-RAY DIFFRACTION16chain 'B' and (resid 78 through 90 )
17X-RAY DIFFRACTION17chain 'B' and (resid 91 through 99 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 8 )
19X-RAY DIFFRACTION19chain 'G' and (resid 7 through 91 )
20X-RAY DIFFRACTION20chain 'G' and (resid 92 through 125 )
21X-RAY DIFFRACTION21chain 'G' and (resid 126 through 169 )
22X-RAY DIFFRACTION22chain 'G' and (resid 170 through 225 )
23X-RAY DIFFRACTION23chain 'G' and (resid 226 through 293 )

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