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- PDB-8tmu: HLA-B*73:01 bound to a 10mer peptide in complex with KIR2DL2 -

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Basic information

Entry
Database: PDB / ID: 8tmu
TitleHLA-B*73:01 bound to a 10mer peptide in complex with KIR2DL2
Components
  • Beta-2-microglobulin
  • HLA-B*73:01
  • KP1
  • Killer cell immunoglobulin-like receptor 2DL2
KeywordsIMMUNE SYSTEM / HLA / MHC / KIR / Class I
Function / homology
Function and homology information


immune response-regulating signaling pathway / antigen processing and presentation / 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 / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion ...immune response-regulating signaling pathway / antigen processing and presentation / 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 / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / MHC class II protein complex / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / 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, 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 / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
DI(HYDROXYETHYL)ETHER / MHC class I antigen / Killer cell immunoglobulin-like receptor 2DL2 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRoss, P. / Adams, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Structure of the archaic HLA molecule HLA-B*73:01
Authors: Ross, P. / Adams, E.J.
History
DepositionJul 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-B*73:01
B: Beta-2-microglobulin
C: Killer cell immunoglobulin-like receptor 2DL2
E: KP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,68711
Polymers69,7714
Non-polymers9177
Water1,08160
1
A: HLA-B*73:01
B: Beta-2-microglobulin
E: KP1
hetero molecules

C: Killer cell immunoglobulin-like receptor 2DL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,68711
Polymers69,7714
Non-polymers9177
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z+1/41
Buried area7410 Å2
ΔGint-14 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.690, 92.690, 200.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein HLA-B*73:01


Mass: 32047.340 Da / Num. of mol.: 1 / Mutation: C271L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A583ZBV1
#2: Protein Beta-2-microglobulin


Mass: 11936.408 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
#3: Protein Killer cell immunoglobulin-like receptor 2DL2


Mass: 24734.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR2DL2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P43627

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Protein/peptide / Sugars , 2 types, 3 molecules E

#4: Protein/peptide KP1


Mass: 1052.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#7: 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: obtained synthetically / 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

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Non-polymers , 3 types, 65 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl pH 8.75 and 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→54.3 Å / Num. obs: 20180 / % possible obs: 99.97 % / Redundancy: 16.8 % / Biso Wilson estimate: 68.74 Å2 / CC1/2: 1 / Net I/σ(I): 11.9
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 1973 / CC1/2: 0.411 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487+SVNrefinement
iMOSFLM7.4.0data reduction
Aimless0.7.7data scaling
PHASER1.20.1_4487+SVNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→54.3 Å / SU ML: 0.4149 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3412
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 999 4.95 %
Rwork0.2155 19178 -
obs0.2177 20177 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.27 Å2
Refinement stepCycle: LAST / Resolution: 2.9→54.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4635 0 59 60 4754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264827
X-RAY DIFFRACTIONf_angle_d0.54966556
X-RAY DIFFRACTIONf_chiral_restr0.0446686
X-RAY DIFFRACTIONf_plane_restr0.0045862
X-RAY DIFFRACTIONf_dihedral_angle_d6.0734674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.050.35171430.32542657X-RAY DIFFRACTION99.96
3.05-3.240.38741230.28612705X-RAY DIFFRACTION100
3.24-3.490.29741440.25372671X-RAY DIFFRACTION100
3.49-3.850.33071520.22932714X-RAY DIFFRACTION100
3.85-4.40.21621520.18322722X-RAY DIFFRACTION100
4.4-5.550.20611270.1682784X-RAY DIFFRACTION100
5.55-54.30.23111580.21672925X-RAY DIFFRACTION99.81
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)
12.096816895841.14031699664-1.685139333595.0325520922-1.592656091424.434414708930.02797340877460.0631216708509-0.0175610113741-0.240831398883-0.274609915714-0.141775745349-0.7128142574060.1290191173220.2487400498470.681610041848-0.0291690266057-0.1743508953720.473315060682-0.05842870156490.43143359802214.18151031812.826519471837.0453807883
20.981452133023-0.003916816052670.6930892585221.584316944961.6190169493.86920725512-0.02218913601520.2851783744720.112356288768-0.596036377243-0.3653822013270.515838541521-0.679620989626-0.8552803868130.4654048588980.7898576804240.24211315328-0.167182821330.824804027996-0.1419110130860.676846450481-3.23502697729.3349974874624.5074924864
33.08558731512-0.229470326825-0.6963992482012.78890334940.7220258829611.99517916214-0.03252303761070.13230344275-0.604137330704-0.442852224396-0.6222869236580.152981314003-0.411296782136-0.4442766400880.1082475460530.480316774011-0.0250397975766-0.01879498958170.350656929624-0.107681924880.4819406727992.45749479651-4.5525742590729.6200352222
47.155222907171.680782693451.096094230942.07777920317-1.636470337684.85487797917-0.402913818052.02283779122-0.472609762439-1.807385558240.1807204248310.199091122776-0.59448952613-0.9714620442950.280706895821.03047415410.201206416608-0.02797989760350.973964190215-0.1318170001570.4716006201188.4438985366-5.106611450317.15353217142
51.740251674261.912903259360.3241539175184.80690089698-0.7285121107940.496213388851-0.1073396370471.08579625966-0.89978817697-0.52231920626-0.540150552978-0.166539059932-0.495825831474-0.4806638629060.1057195154720.5162510457310.119924820023-0.08861865339480.65301325719-0.1976702277840.3022644038988.39352996088-3.3345517244621.4490448246
68.10561696217-5.11102317159-0.6466628755894.092274414541.415311569092.41899838523-0.552199956737-1.02223733813-0.489081113141.035822480450.88465925777-0.3952354824111.173753713691.724591031620.02388624111140.541672470897-0.0734396702692-0.01191942212160.329176152046-0.06075364034940.50433464822411.8521387743-8.1648557481230.475959894
79.20960221634-6.61617091178-3.964419900294.75742931212.881198644212.797697444550.0133280584811-0.282825646374-0.363627561966-0.001720383856490.315188259258-1.743604549090.274382248432-0.4469139548960.1582717924340.5777141856840.0152222337631-0.07716738092640.521198995104-0.01723706203710.43039984507818.3422891974-10.517774966621.568202855
82.53669525314-2.00951980341-1.653909645766.437458945211.750099685962.271261093030.5775467476310.301365598255-0.220567469376-0.301741639565-0.432782302618-0.185199579564-0.84530879503-0.603889191477-0.07234955706520.5688583729840.0749967478156-0.1866896260090.515379867899-0.1122145034930.472200283449.483884648831.5495193741327.3962221001
93.46358233536-0.194479983387-0.915979029784.785260206376.653021383839.47447059730.1361243653271.26226948602-1.64827468191-1.11882330854-0.7442850406480.8466786549981.79790247856-1.384073935220.6479004843160.743150045503-0.169970947338-0.07469088200191.07235376196-0.3791117731391.023771330019.14263508749-17.83025889669.37867935454
106.79698159445-5.63775943651-6.478411795718.60686234457.198908054397.01402008782-0.95136351953-0.02449953782640.1638669804050.02657094479830.123014898087-0.230832945809-0.0892482965834-0.4463154411690.8213102315930.458221119924-0.0176019415034-0.03683953443040.514544703985-0.05037144361280.5523087027959.96373893861-13.11474964525.074558569
113.002025561321.03738354437-3.606103022054.738800595723.121871779898.64088431759-0.2241511627360.651777327587-0.0216486445365-0.151705372186-0.117993410073-0.09984069581130.0346214725734-1.103543139520.06077643357160.419559770960.00192836373776-0.1575942329620.673389158146-0.1686963704770.7299856330363.75906803775-12.432782162425.1261968813
127.518627932582.532515711150.3356219139246.363873177080.8638502238942.431026316570.00179872287497-0.1354687291680.3865928338510.0960311184058-0.2067306771580.032098454168-0.398226220439-0.1219285586820.1566793420080.4555615099030.0787718436032-0.07888954212990.518110755152-0.0793646430050.40474125943533.3374665808-10.403686335114.8146446405
133.551792199822.4791796425-1.809377012932.44284527562-0.8466110439321.68114548961-0.200518939995-0.280436384644-0.5077910143290.153142872269-0.146910610719-0.440283871167-0.02872135935870.1462532182120.1781767364830.3662826490750.0787071355057-0.07093118619610.486424231695-0.0896198553630.44691503697223.715852914-25.091243847320.9233219396
145.222900647680.939766745822-2.312668750582.13478148748-0.68396325163.91908099629-0.184253575545-0.436612273510.1858186471550.105784542270.0699841620177-0.245779540420.07882536990250.4809499190290.02265411556360.4228119130060.115151063827-0.05987336912610.667617392065-0.1684507167850.53740958938117.4260239827-33.503380059722.4538541664
154.86978005489-1.1632332512-1.533133622981.5478882331-1.37683384568.297456663050.387752467997-0.531672861442-0.373444969680.4554127935850.3660213441230.423349207416-1.198880432711.02502972226-0.1977720052270.904877060893-0.000294070190703-0.2780819043480.6681548178950.163740495160.87793593370414.776750639220.441654940343.5853098536
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 118 )AA1 - 1181 - 118
22chain 'A' and (resid 119 through 276 )AA119 - 276119 - 275
33chain 'B' and (resid 2 through 12 )BF2 - 121 - 11
44chain 'B' and (resid 13 through 20 )BF13 - 2012 - 19
55chain 'B' and (resid 21 through 31 )BF21 - 3120 - 30
66chain 'B' and (resid 32 through 42 )BF32 - 4231 - 41
77chain 'B' and (resid 43 through 52 )BF43 - 5242 - 51
88chain 'B' and (resid 53 through 72 )BF53 - 7252 - 71
99chain 'B' and (resid 73 through 78 )BF73 - 7872 - 77
1010chain 'B' and (resid 79 through 84 )BF79 - 8478 - 83
1111chain 'B' and (resid 85 through 100 )BF85 - 10084 - 99
1212chain 'C' and (resid 1 through 82 )CH1 - 821 - 82
1313chain 'C' and (resid 83 through 130 )CH83 - 13083 - 130
1414chain 'C' and (resid 131 through 204 )CH131 - 204131 - 204
1515chain 'E' and (resid 1 through 10 )EK1 - 101 - 10

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