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- PDB-9k2s: Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA... -

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Basic information

Entry
Database: PDB / ID: 9k2s
TitleKiller cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*1202 and IY10 peptide
Components
  • Beta-2-microglobulin
  • KIR2DL2
  • MHC class I antigen
  • peptide from p51 RT
KeywordsIMMUNE SYSTEM / CD8+ T cells / HIV-1 / escape mutant / KIR2DL2 / TCR / HLA
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / HIV-1 retropepsin ...antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / HIV-1 retropepsin / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / symbiont-mediated activation of host apoptosis / peptide antigen assembly with MHC class II protein complex / retroviral ribonuclease H / exoribonuclease H / cellular response to iron(III) ion / MHC class II protein complex / exoribonuclease H activity / 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 / DNA integration / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / host multivesicular body / cellular response to nicotine / viral genome integration into host DNA / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / specific granule lumen / viral penetration into host nucleus / phagocytic vesicle membrane / recycling endosome membrane / RNA-directed DNA polymerase activity / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RNA-DNA hybrid ribonuclease activity / negative regulation of epithelial cell proliferation / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / host cell / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / DNA recombination / protein homotetramerization / amyloid fibril formation / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis / DNA-directed DNA polymerase activity / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / symbiont-mediated suppression of host gene expression / Golgi membrane / viral translational frameshifting / lysosomal membrane / external side of plasma membrane / focal adhesion / lipid binding / Neutrophil degranulation / symbiont entry into host cell / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / proteolysis / extracellular space
Similarity search - Function
: / Immunoglobulin / Immunoglobulin domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / Reverse transcriptase thumb ...: / Immunoglobulin / Immunoglobulin domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / Reverse transcriptase thumb / Reverse transcriptase thumb domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
MHC class I antigen / Gag-Pol polyprotein / Beta-2-microglobulin / KIR2DL2
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChikata, T. / Kuroki, K. / Kuse, N. / Kliszczak, A. / Paes, W. / Tomioka, N. / Parker, R. / Aflalo, A. / Akahoshi, T. / Yamashita, R. ...Chikata, T. / Kuroki, K. / Kuse, N. / Kliszczak, A. / Paes, W. / Tomioka, N. / Parker, R. / Aflalo, A. / Akahoshi, T. / Yamashita, R. / Sakata, R. / Kusaka, H. / Watanabe, Y. / Nicastri, A. / Matsubara, H. / Ose, T. / Kita, S. / Oka, S. / Gatanaga, H. / Lin, Z. / Ternette, N. / Borrow, P. / Maenaka, K. / Takiguchi, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)20H03726 Japan
Japan Society for the Promotion of Science (JSPS)17fk0410302h0003 Japan
Japan Society for the Promotion of Science (JSPS)21fk0410032h0003 Japan
CitationJournal: To Be Published
Title: Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*1202 and IY10 peptide
Authors: Chikata, T. / Kuroki, K. / Kuse, N. / Kliszczak, A. / Paes, W. / Tomioka, N. / Parker, R. / Aflalo, A. / Akahoshi, T. / Yamashita, R. / Sakata, R. / Kusaka, H. / Watanabe, Y. / Nicastri, A. ...Authors: Chikata, T. / Kuroki, K. / Kuse, N. / Kliszczak, A. / Paes, W. / Tomioka, N. / Parker, R. / Aflalo, A. / Akahoshi, T. / Yamashita, R. / Sakata, R. / Kusaka, H. / Watanabe, Y. / Nicastri, A. / Matsubara, H. / Ose, T. / Kita, S. / Oka, S. / Gatanaga, H. / Lin, Z. / Ternette, N. / Borrow, P. / Maenaka, K. / Takiguchi, M.
History
DepositionOct 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: peptide from p51 RT
A: MHC class I antigen
B: Beta-2-microglobulin
C: KIR2DL2


Theoretical massNumber of molelcules
Total (without water)69,0494
Polymers69,0494
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.493, 44.585, 88.243
Angle α, β, γ (deg.)90.000, 111.450, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide peptide from p51 RT


Mass: 1156.373 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
References: UniProt: P12499
#2: Protein MHC class I antigen


Mass: 32004.137 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 (E. coli) / References: UniProt: A0A165EYK7
#3: Protein Beta-2-microglobulin


Mass: 13718.520 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 (E. coli) / References: UniProt: P61769
#4: Protein KIR2DL2 / Killer cell immunoglobulin like receptor / two Ig domains and long cytoplasmic tail 2 / Killer cell ...Killer cell immunoglobulin like receptor / two Ig domains and long cytoplasmic tail 2 / Killer cell immunoglobulin-like receptor 2DL2 / Killer cell immunoglobulin-like receptor two domains long cytoplasmic tail 2


Mass: 22169.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR2DL2, KIR2DL3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N742
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M K/Na tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.61 Å / Num. obs: 22791 / % possible obs: 93.7 % / Redundancy: 10.1 % / Biso Wilson estimate: 28.31 Å2 / CC1/2: 0.985 / Net I/σ(I): 10.1
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 2274 / CC1/2: 0.886

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.61 Å / SU ML: 0.3188 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.3822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2994 1163 5.11 %
Rwork0.2446 21618 -
obs0.2474 22781 93.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.62 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4567 0 0 144 4711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084692
X-RAY DIFFRACTIONf_angle_d1.1516365
X-RAY DIFFRACTIONf_chiral_restr0.0622655
X-RAY DIFFRACTIONf_plane_restr0.0112836
X-RAY DIFFRACTIONf_dihedral_angle_d16.4741724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.37041240.31612616X-RAY DIFFRACTION90.61
2.51-2.640.36261440.31692710X-RAY DIFFRACTION94.85
2.64-2.810.39281380.30212751X-RAY DIFFRACTION95.13
2.81-3.020.33561510.292684X-RAY DIFFRACTION94.85
3.02-3.330.32571480.26542715X-RAY DIFFRACTION94.68
3.33-3.810.29281510.23152723X-RAY DIFFRACTION93.59
3.81-4.80.21941290.18542691X-RAY DIFFRACTION92.55
4.8-48.610.27111780.21022728X-RAY DIFFRACTION91.41
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)
17.519239591564.00613319494.802795231195.130805771963.256988741943.22859279321-0.7135183306880.3622041174020.287160465051-0.5072252039610.4230639344240.5235403691-0.1518540286520.578048509360.2615678381880.18881070588-0.009248652080090.01508245232520.348513313370.08285282375210.30557831716819.84519037862.035066743-17.7186384101
25.587698749452.03549150373-0.3019557434822.21274690478-0.3166461131411.109041274620.002193575292120.2450650734590.725050380248-0.08074906516360.008625642960780.293084960354-0.257420633916-0.0739333371007-0.0349780660110.2337052218460.0205133186044-0.01135126222060.1531385470470.008678377366870.22157828525120.342757128710.7758237115-10.1835644673
33.959937916441.61478065819-0.07518225244490.8071589524750.3114965462111.073161489520.2541157416240.0115922948969-0.2828825434410.0742075066211-0.1404288165240.01734109068870.005937935203860.0369786369805-0.1110323991650.1785394176240.0378076803732-0.01068165101650.1122541967860.01509246953580.20839214208420.4795410809-5.6860876219-10.5970665603
40.728461295429-0.2518980304130.4439478034780.8541970633760.5914559032396.82298353332-0.0140237354507-0.179636775957-0.09057530581260.1153952777680.0735529662098-0.09365398054950.5640533992040.274824641287-0.04018806152670.144844693960.0105545555479-0.02431573215550.2056522618520.007735453210760.25113967916137.91543566156.2971315090817.2981435754
52.51401339944-0.384768726525-0.4799775475963.20721552876-0.5072848627423.34084929772-0.0417382577199-0.30358012181-0.1714815546-0.1285980292130.0875217401910.0914928438080.06611904732030.1583339596410.003852969862670.235726906407-0.0006919985218550.122289014680.235367236376-0.06753391600760.16599855292724.131426464914.528332863515.5057029685
61.859785136513.312408135731.604927114817.018452694373.321824778162.98161691628-0.302252403789-0.1701973331540.145532284266-0.5013906496590.008805918777750.313971592018-0.177695536013-0.2756427566780.2832813329970.1603319368090.007954512743740.02505345190130.281344441322-0.02628564954090.16888505850918.090520268515.5043107911.0345784959
73.913227624380.254242623004-0.202459734664.183710358723.550984012413.102996209590.1324965353570.1352245651980.2382588310390.1087592587920.195309297152-0.1486868857-0.1196515088880.117447567832-0.3281628679190.2271145365810.0191662440329-0.009216469890760.1780104486660.06386487462120.12102135318719.844252792316.42768018797.7502469292
81.987359245184.031605512332.63390040339.195154720844.464660648978.897059330870.035223122189-2.002609243190.8386291115641.731639841680.140580583203-0.5079014068410.518202542440.802143231934-0.1883792058890.5260481879050.0907487109096-0.09951296746160.611032610614-0.1984497951750.40810216388723.349967132828.591451065125.5297253692
94.111700187680.8677586162810.5125609015138.467207481372.750984326943.79469389208-0.0415648364422-0.5383954414-0.1290466222430.327648552881-0.2308791931581.03839859739-0.0599523967459-0.4986161246430.3098745697290.1886926248430.02732761491380.02529458903270.248401810051-0.01607313691130.26798313482210.568432910813.326272135115.8079291122
103.16340370541.19898441902-3.387009196843.54289298097-2.551688712994.14488952522-0.145698587582-1.10344680264-0.1326939890470.470560133155-0.074656150008-0.0451737118796-0.3814664717040.1372564736960.2295638004160.2405489851510.08041765554330.06085262287910.368757810342-0.02627251733330.14997012503522.36768782516.219799010323.060180977
112.98319397932-1.012246235740.7291746405082.43715733488-0.02023900561822.713320752190.08341526491490.1633568118160.164264524914-0.216838298944-0.0928315444818-0.144832316789-0.254325127612-0.310436584220.02208864172080.240375704056-0.006413357014580.09382390019490.2038337182290.01005572623510.200359203948-5.168804234210.4572589996-31.5452652688
122.597977995280.8383596950722.521430355942.649573143571.096521485835.249670262830.08696409446270.436858042467-0.1773586414590.1003401854370.0925395167622-0.2048146222290.5852159165410.492698763355-0.140798522850.2091060286070.005572305564680.0460933476260.207155637417-0.05616435684280.2754938333038.06023222249-16.6715362854-36.2030557746
131.551123026110.70741187787-1.269627503942.952685300581.308534423653.52245752572-0.09568473240830.0564490940896-0.0812057843585-0.2057764840380.028375971947-0.2620188605570.0858091489755-0.2221650896640.01280399856590.306956611934-0.007291369074550.006338362970580.161289579476-0.00984237063560.284670924425.30094494678-13.6528831423-34.0720997231
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 1 through 10 )DA1 - 101 - 10
22chain 'A' and (resid 4 through 85 )AB4 - 851 - 80
33chain 'A' and (resid 86 through 163 )AB86 - 16381 - 158
44chain 'A' and (resid 164 through 277 )AB164 - 277159 - 272
55chain 'B' and (resid 2 through 20 )BC2 - 201 - 19
66chain 'B' and (resid 21 through 42 )BC21 - 4220 - 41
77chain 'B' and (resid 43 through 72 )BC43 - 7242 - 71
88chain 'B' and (resid 73 through 78 )BC73 - 7872 - 77
99chain 'B' and (resid 79 through 91 )BC79 - 9178 - 90
1010chain 'B' and (resid 92 through 100 )BC92 - 10091 - 99
1111chain 'C' and (resid 7 through 102 )CD7 - 1021 - 91
1212chain 'C' and (resid 103 through 140 )CD103 - 14092 - 129
1313chain 'C' and (resid 141 through 200 )CD141 - 200130 - 183

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