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- PDB-9bla: KIR3DL1*086 in complex with HLA-A*24:02 presenting the NEF peptide -

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Basic information

Entry
Database: PDB / ID: 9bla
TitleKIR3DL1*086 in complex with HLA-A*24:02 presenting the NEF peptide
Components
  • Beta-2-microglobulin
  • C-terminal core peptide
  • Killer cell immunoglobulin-like receptor 3DL1
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / immunoglobulin fold / natural killer cell receptor / Kir
Function / homology
Function and homology information


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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion ...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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / 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 / 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 / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / 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 / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / 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 / 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 / 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 / KIR3DL1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFaoro, C. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2008981 Australia
CitationJournal: Cell / Year: 2024
Title: An archaic HLA class I receptor allele diversifies natural killer cell-driven immunity in First Nations peoples of Oceania.
Authors: Loh, L. / Saunders, P.M. / Faoro, C. / Font-Porterias, N. / Nemat-Gorgani, N. / Harrison, G.F. / Sadeeq, S. / Hensen, L. / Wong, S.C. / Widjaja, J. / Clemens, E.B. / Zhu, S. / Kichula, K.M. ...Authors: Loh, L. / Saunders, P.M. / Faoro, C. / Font-Porterias, N. / Nemat-Gorgani, N. / Harrison, G.F. / Sadeeq, S. / Hensen, L. / Wong, S.C. / Widjaja, J. / Clemens, E.B. / Zhu, S. / Kichula, K.M. / Tao, S. / Zhu, F. / Montero-Martin, G. / Fernandez-Vina, M. / Guethlein, L.A. / Vivian, J.P. / Davies, J. / Mentzer, A.J. / Oppenheimer, S.J. / Pomat, W. / Ioannidis, A.G. / Barberena-Jonas, C. / Moreno-Estrada, A. / Miller, A. / Parham, P. / Rossjohn, J. / Tong, S.Y.C. / Kedzierska, K. / Brooks, A.G. / Norman, P.J.
History
DepositionApr 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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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: C-terminal core peptide
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0246
Polymers78,5824
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.682, 61.790, 67.473
Angle α, β, γ (deg.)93.726, 100.679, 108.337
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#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 / Details (production host): pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A411J078
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Details (production host): pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide C-terminal core peptide


Mass: 1040.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Protein Killer cell immunoglobulin-like receptor 3DL1


Mass: 33884.242 Da / Num. of mol.: 1 / Fragment: residues 1-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1 / Production host: Homo sapiens (human) / References: UniProt: I6LEK9
#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.: 2
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
Has ligand of interestN
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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 14% PEG 3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium 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: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 3→46.96 Å / Num. obs: 14821 / % possible obs: 97.9 % / Redundancy: 2.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.045 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2422 / CC1/2: 0.965

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5058refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→46.96 Å / SU ML: 0.4568 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 32.2443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2477 737 4.97 %
Rwork0.2 14084 -
obs0.2024 14821 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.69 Å2
Refinement stepCycle: LAST / Resolution: 3→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4993 0 28 0 5021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00255170
X-RAY DIFFRACTIONf_angle_d0.53227037
X-RAY DIFFRACTIONf_chiral_restr0.0409746
X-RAY DIFFRACTIONf_plane_restr0.0047916
X-RAY DIFFRACTIONf_dihedral_angle_d11.17511810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.230.32931330.2792836X-RAY DIFFRACTION98.25
3.23-3.560.31251600.2332832X-RAY DIFFRACTION98.62
3.56-4.070.24721430.20872809X-RAY DIFFRACTION97.75
4.07-5.130.23591520.17712845X-RAY DIFFRACTION98.17
5.13-46.960.2171490.18282762X-RAY DIFFRACTION96.26
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)
10.175138863756-0.2637968070980.09422642888890.382140979811-0.5000159372811.657431032890.006654236646240.3332143628890.230932243411-0.04530430351580.239641530006-0.1309497271890.153861708906-0.1060278104320.00806159088310.3683986040370.05888018383130.1106886712690.423346010311-0.1767161475650.4940218911925.4875.571-9.124
20.02654845654750.081345080479-0.1015210422930.597502932035-0.490248398430.2668575783750.3387572262430.166130703679-0.0888162986722-1.105547689410.1055879078960.186352753053-0.266286835516-0.07507480892070.01332076191890.5316534097490.1159668834670.08522307247560.599319927990.02769801980810.641664081563-1.45614.411-15.037
30.379280479526-0.00862014488085-0.1355995655220.320048480656-0.4206237030581.39373422319-0.00548160450333-0.113444574051-0.2468168554380.4001618032050.599753846910.3325905370220.548492302946-0.7777039249520.07876296359650.580390361966-0.15457192945-0.04003173280930.7579699486710.1032292892690.683912558637-11.635.431-9.605
40.06332896075880.0954370732447-0.2531697580860.767058651957-0.820477252340.887933182397-0.01037578748160.314336494804-0.135353329683-0.6062133782830.4743397373880.2537905022650.755330759135-0.6819378052760.1201248933770.59706399294-0.0438133293042-0.09266786674750.7964691572380.09496341565870.726131599322-9.5152.648-19.212
50.4548578234780.00311729688327-0.0310942400751-0.00245170156884-0.1219287956640.1666968491860.120734343531-0.345408831552-0.571015030149-0.138887903010.1695602198080.1036595553030.1783990939121.05170779698-0.0005434631609511.07396753959-0.0559033428306-0.1283036579020.760026659414-0.02112435007380.7584561677716.154-15.6849.812
61.73002840150.686166538287-0.8714143836340.382463342951-0.3820824248040.5274808570130.136895908858-0.2057936951880.0869982695909-0.2954187824490.0835100476329-0.07071669993840.27520560452-0.5225607838590.000161345932860.792400774436-0.0853538743863-0.06690255500110.6119784445720.03930315197590.585987880565-0.845-16.46214.542
70.6198211956020.7225221150590.2799403646882.40801887626-1.076232797261.25472393420.1972404172520.157285830719-0.0737415958791-0.2695528286080.6546957610110.08429907375230.652057056779-0.3486197941860.299734614860.608525544156-0.09108403420270.07698827083260.779554544408-0.02531465832930.380552195842-1.4125.50710.988
80.3461340771270.6349055009350.02578271968571.183253278440.04476116328660.001453397697260.191584027330.175573333492-0.356297700529-0.2570061611350.810051928192-0.7592454337980.5434921918050.702687095458-0.02415227408280.7955462757690.199985807741-0.2787882489411.073515873390.0845260507771.1088125468618.818-8.90813.758
90.7298617580340.5096093308140.2111819472020.4199284424370.05650586647990.2145666138281.17858379094-0.141892077685-0.4928865999840.341034755064-0.596816403345-0.0445170025465-0.01809853885510.1692736831280.1722836933270.5748621091380.1003439088990.004106690292120.471191935028-0.000265816082930.5172127899458.8440.9069.402
100.1640810352260.181504338367-0.2041237036370.163329244595-0.2391937368790.234978115595-0.0490629400243-0.03539624996570.2229852467630.794875332377-0.487745946597-0.244078269296-0.760835179838-0.09980199999190.000303607211980.9765286654150.108199858797-0.2407199625350.708000697144-0.01451806090750.9024658340256.07411.189.977
110.16626184352-0.0940304214153-0.1703213452980.04725750609490.09004786591810.143387919605-0.6930760322540.384946052270.756994686540.6174797301070.0634317892377-0.8143849466660.3675278530530.166200537808-0.001074463786570.808551990197-0.0460789191057-0.1547986235140.8282166388960.08782740231731.0162866100817.489.32811.604
120.2181495865880.0884165414541-0.03466627476430.121322864812-0.2390030692030.3431580750980.6391102336860.269028627841-0.03221842362560.0607500517374-0.419956459481-0.232789463636-0.03697908720630.229058087085-0.000496130006030.521814056771-0.0278262072451-0.04471013994950.584462825087-0.005714989260810.3740800355334.8063.6453.393
130.06500768759490.101792915111-0.1109118800490.159978858153-0.1707879635570.1885576799380.579815840959-0.197244854565-0.3724083562380.4761841630490.664721459027-0.206834258546-0.3090542138240.2991658820820.008594496127020.8331928046810.356678466389-0.3224905417061.8118169290.1511620542621.4592013023521.046-0.54723.265
143.400984996120.06303053749020.9960568529952.38225841957-1.256334601071.931601633190.303868455185-0.08905084404940.001371139969041.07104601673-0.255340007657-0.379398986924-0.79480533314-0.975519893012-0.1230373005781.158263258570.2726539534940.07305489376310.472508184409-0.1224784092630.4778802464024.43411.55215.78
15-0.001160982883360.02034841880220.008828606281240.05801788939420.0545781808280.05097290414410.682569904293-0.0870717002347-0.1782549823220.22766506744-0.7686708865050.520993956691-0.1572066666550.5244025506670.0008456354043671.049029476150.179825173721-0.04821941497490.7631946459920.01957660699720.7017244090829.221-1.2220.982
160.260932723912-0.1078405918860.1647443698590.0368579320343-0.04189605403220.0768769953716-0.4333767112370.965138412143-0.8541270111620.28910319413-0.08168551019331.02772819036-0.384550369450.325223092528-4.73142454974E-50.4354907292170.06150004725750.03660721143950.671970092891-0.03094597230180.646272230049-5.168.824-17.511
171.324382899351.123040615790.4582612469240.8774326584950.9741197194551.48507530008-0.058738249843-0.3048812912850.1417809443280.229078111827-0.0328041687199-0.189554716518-0.724523658107-0.0512913777452-0.00015577660730.6924214511890.0428690213773-0.014891150150.507638227455-0.01647788790520.6498651921529.23138.51-1.961
181.52547597004-1.002588136691.424679687011.33058293686-1.453119276741.63100507315-0.4150387371910.0470975380160.001160325933720.372618622840.0644664165553-0.367616576625-0.645080648923-0.0766682342814-0.06369013821580.5981092332610.01199490281360.02321250498260.604010513831-0.02112849897160.566400388408-3.0834.744-26.612
191.78435760716-0.2798599969360.7613670499030.8113693879270.6735948137883.553626527730.879977363156-0.42188772305-0.2875071123040.1634436469850.4542098185270.160603933821-0.440987657882-1.363496820253.54125188879-0.5046806353440.2020083087570.449952485381.250945914440.57944684070.787361089193-24.37623.916-27.522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:56 )A1 - 56
2X-RAY DIFFRACTION2( CHAIN A AND RESID 57:85 )A57 - 85
3X-RAY DIFFRACTION3( CHAIN A AND RESID 86:137 )A86 - 137
4X-RAY DIFFRACTION4( CHAIN A AND RESID 138:174 )A138 - 174
5X-RAY DIFFRACTION5( CHAIN A AND RESID 175:197 )A175 - 197
6X-RAY DIFFRACTION6( CHAIN A AND RESID 198:276 )A198 - 276
7X-RAY DIFFRACTION7( CHAIN B AND RESID 0:11 )B0 - 11
8X-RAY DIFFRACTION8( CHAIN B AND RESID 12:19 )B12 - 19
9X-RAY DIFFRACTION9( CHAIN B AND RESID 20:30 )B20 - 30
10X-RAY DIFFRACTION10( CHAIN B AND RESID 31:41 )B31 - 41
11X-RAY DIFFRACTION11( CHAIN B AND RESID 42:51 )B42 - 51
12X-RAY DIFFRACTION12( CHAIN B AND RESID 52:71 )B52 - 71
13X-RAY DIFFRACTION13( CHAIN B AND RESID 72:77 )B72 - 77
14X-RAY DIFFRACTION14( CHAIN B AND RESID 78:90 )B78 - 90
15X-RAY DIFFRACTION15( CHAIN B AND RESID 91:99 )B91 - 99
16X-RAY DIFFRACTION16( CHAIN C AND RESID 1:8 )C1 - 8
17X-RAY DIFFRACTION17( CHAIN G AND RESID 7:108 )G7 - 108
18X-RAY DIFFRACTION18( CHAIN G AND RESID 109:219 )G109 - 219
19X-RAY DIFFRACTION19( CHAIN G AND ( RESID 220:291 OR RESID 401:402 ) )G220 - 291
20X-RAY DIFFRACTION19( CHAIN G AND ( RESID 220:291 OR RESID 401:402 ) )G401 - 402

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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