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- PDB-7nui: Crystal structure of HLA-B*08:01 in complex with ELRSRYWAI viral ... -

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Basic information

Entry
Database: PDB / ID: 7nui
TitleCrystal structure of HLA-B*08:01 in complex with ELRSRYWAI viral peptide
Components
  • Beta-2-microglobulin
  • GLU-LEU-ARG-SER-ARG-TYR-TRP-ALA-ILE
  • HLA-B*08:01 heavy chain
KeywordsPEPTIDE BINDING PROTEIN / Major Histocompatibility complex class I HLA-B
Function / homology
Function and homology information


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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / 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 / 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 / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Beta-2-Microglobulin / 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 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMavridis, G. / Giastas, P. / Mpakali, A.
Funding support Greece, 1items
OrganizationGrant numberCountry
Hellenic Foundation for Research and Innovation (HFRI)157 Greece
CitationJournal: To Be Published
Title: Crystal structure of HLA-B*08:01 in complex with ELRSRYWAI viral peptide
Authors: Mavridis, G.
History
DepositionMar 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: HLA-B*08:01 heavy chain
B: Beta-2-microglobulin
D: GLU-LEU-ARG-SER-ARG-TYR-TRP-ALA-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3598
Polymers45,0053
Non-polymers3545
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint9 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.236, 40.206, 125.978
Angle α, β, γ (deg.)90.000, 101.530, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA-B*08:01 heavy chain


Mass: 31930.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#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 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules D

#3: Protein/peptide GLU-LEU-ARG-SER-ARG-TYR-TRP-ALA-ILE


Mass: 1195.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide from Influenza A virus protein / Source: (synth.) Influenza A virus

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Non-polymers , 3 types, 103 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M sodium iodide, 0.1 M Bis-Tris propane, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→44.54 Å / Num. obs: 30185 / % possible obs: 99.25 % / Redundancy: 3.4 % / Biso Wilson estimate: 44.12 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 30316
Reflection shellResolution: 2→10 Å / Rmerge(I) obs: 0.2 / Num. unique obs: 30184

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WMQ

5wmq


Resolution: 2→44.54 Å / SU ML: 0.4007 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.0443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2823 1526 5.06 %
Rwork0.2296 28659 -
obs0.2322 30185 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.63 Å2
Refinement stepCycle: LAST / Resolution: 2→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 23 98 3249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823245
X-RAY DIFFRACTIONf_angle_d1.09954405
X-RAY DIFFRACTIONf_chiral_restr0.059449
X-RAY DIFFRACTIONf_plane_restr0.0069584
X-RAY DIFFRACTIONf_dihedral_angle_d14.5862447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.43051220.42022531X-RAY DIFFRACTION97.04
2.06-2.140.44271500.39442606X-RAY DIFFRACTION99.57
2.14-2.220.36821400.35662564X-RAY DIFFRACTION99.59
2.22-2.330.39751210.35652576X-RAY DIFFRACTION99.34
2.33-2.450.39411510.33442612X-RAY DIFFRACTION99.86
2.45-2.60.37471510.31212583X-RAY DIFFRACTION99.31
2.6-2.80.36741350.31672569X-RAY DIFFRACTION98.94
2.8-3.080.29181370.24042648X-RAY DIFFRACTION99.71
3.08-3.530.29561290.21072620X-RAY DIFFRACTION99.71
3.53-4.450.21941480.16962639X-RAY DIFFRACTION99.79
4.45-44.540.22991420.17862711X-RAY DIFFRACTION98.99
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)
11.755796748410.221989730723-0.4864677875183.141593841310.1531476518774.5282988137-0.12870302131-0.8632690254940.6132718038580.321436573711-0.1035315520560.0103254861498-1.016895161080.1604534002820.02556703412850.704112417868-0.1063354088230.006402220170990.3853746719320.03819641688690.314083320121-18.318099424919.123627709719.0594812837
24.5087356306-3.95648338354-0.4922803448045.504380998640.5050925977160.0826915468468-0.500220256507-1.328068281931.052691474151.070307401280.169297127486-0.242571743097-1.764809722880.410117970080.04824076516681.57871919366-0.197925161608-0.109494601210.661683725171-0.1123145213590.604832255339-14.521827743326.861685226224.0168823941
31.552105711990.0946646810117-1.225145475993.40585594867-1.86082414812.18846054033-0.0904505883552-0.1503367005130.5986133488680.903051292599-0.16934465786-0.213553103905-1.94402591797-0.163632527913-0.05245584049021.29897002695-0.240431770576-0.1962020207340.2300213595870.05722370496150.523318628913-17.936519234225.829321072612.4574319373
41.02295056101-1.086781234751.520659815592.40454342964-0.2442956736377.14902258637-0.1417079493870.2665059725140.0361073411725-0.193372783041-0.0617067893118-0.222194795611-0.1288903124041.001710874170.2196485074620.594154477838-0.1114051669130.01055472926870.3760077009040.06428789448810.339978487104-13.104716882111.95603709688.79380240392
51.68043788310.717064086431-0.94996586211.543455509130.6161884312995.89868936198-0.292673745477-0.0497010860729-0.4190418380320.2115000904290.0512511940661-0.527926947118-0.7957545373981.233129119430.5197702412160.286328070254-0.0559007041911-0.1319055417841.020546960510.06714436305850.779734844256-1.603388662610.273508676543.3735131901
65.89049140638-1.869998010880.9604861101345.32259643057-0.2678480445024.59808324023-0.223746525023-0.181289159073-1.288068554550.301709160204-0.015999782881-0.1628074072270.5107113446440.8115055371750.256931617040.4189681406180.151900218545-0.07705640467520.646943863160.04210544412970.747903554517-1.168607715082.816571013943.6674007344
78.853970969874.939927695535.95217231126.929585522843.428415306328.35295342374-0.523993282922-1.30395673978-1.02651827823-0.6138244070580.38693032298-0.479938449058-0.105376511996-1.07752351096-0.1804845297530.4712690423080.1738444355830.09678163809810.7354603104550.1250075419020.402804268065-20.75980699927.1202760664234.4101888309
83.268612656710.4019653766721.581662772356.718711617452.649565998365.32976798744-0.356421887351-1.901512935690.3238333156121.407879397090.4167038729-0.374952456477-1.535491599240.5998977105210.3754622582421.004820048010.235864071674-0.3087361502871.35163571638-0.1650330061640.682366414721-10.646330653618.78163249852.606278511
94.830234497360.7898215809171.909285630310.238759303373-0.2341367919177.51057840796-0.617054722456-0.876176060840.6677394404580.3383007772940.5227527534970.170481534302-1.70179449914-1.220917526530.2691046455170.7328806681270.294909008478-0.09930479835050.959469680056-0.08467917679160.438845187278-17.679015600715.400567839440.4095694623
100.0288436473130.3057562603750.1813472769065.946092064154.087743468372.85557119381-0.39100587347-1.215617637130.2321702410340.571924968762-0.129389585530.0837835460625-0.25485083948-1.954361613830.3219885712340.7950410577650.330268395622-0.04040481371241.39437946112-0.1352475964410.413116001001-28.322218566315.778737841840.5202190453
115.40648429317-2.97311509515-2.044309050946.710599934786.790779043047.11967667393-0.2907524287840.613066633431.28315706156-0.3715335683020.1962355118070.61613932362-2.04058775412-2.109107445420.1254815426941.403094318980.384145255847-0.2145543738011.01468070815-0.1295166499910.720736321658-24.660405601824.245432361640.7141535104
122.36168473621.61190251891.375820637331.546228904441.457420719321.92322702915-0.721335756663-1.282137833540.434100656020.2367167468590.656632957901-0.150352667061-0.9199167756370.1339001000270.1076546831590.8229782056650.192350666863-0.08030555169650.719347987432-0.08271793687250.380487705201-18.004271313216.246643432932.8778829163
136.6932746009-6.685603617770.7643960077886.94160564070.08316360054212.85420069128-0.5544553519284.13389891020.671672161159-1.33093236898-0.5504911181651.1450687788-1.39636522791-1.182203038110.2261086610171.113127900470.660450127896-0.352641066122.18949902735-0.2240591367570.776214681685-21.044610765714.692128386358.0994324407
144.85259240146-3.309052699551.567205119223.5873348852-0.06719511372416.19816319358-1.17913138164-1.31695045560.05722904113871.031316082320.3711770026010.384249663715-0.6259717564180.03060290393430.272023903090.5822786626810.5447561157510.0217382497651.890971598120.141524001310.595319021319-27.08000224312.629441188943.8743625598
152.97018469428-3.69686466837-1.340722467984.607407853511.842574801952.22959558997-0.267324462629-0.938542663198-0.788443068488-0.1863370828210.1040493340030.6340211372180.128761919174-2.44807019123-0.5079886208590.599706565651-0.1702433235630.03703665968371.089806390330.1346084675060.467615845031-32.21989202115.8753221622734.9168122757
165.939006097730.0967647421811-0.4301146556042.004184803191.868309350560.348260217278-0.415128490822-1.1024324876-0.1559423066891.180273545310.468096730547-1.049758485890.2157981357280.231758620878-0.04605884358450.4594087066740.2988945621820.05143668222211.966711921850.3226342790570.702931125763-19.32390257638.1510944149448.9556503961
175.36800543526-2.1292421476-1.365882924517.08003962987-6.023888187498.82370085087-0.1470386785950.361091169125-0.220991375524-0.36959125629-0.106097735426-0.497384543665-1.366821456530.834249652930.4498216408260.835597825664-0.0677231955752-0.04053468295360.3355753869770.03093353265330.419950806601-16.723373482520.16170826676.0447686469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 174 )
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 276 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 11 )
8X-RAY DIFFRACTION8chain 'B' and (resid 12 through 19 )
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 30 )
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 46 )
11X-RAY DIFFRACTION11chain 'B' and (resid 47 through 51 )
12X-RAY DIFFRACTION12chain 'B' and (resid 52 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 77 )
14X-RAY DIFFRACTION14chain 'B' and (resid 78 through 83 )
15X-RAY DIFFRACTION15chain 'B' and (resid 84 through 90 )
16X-RAY DIFFRACTION16chain 'B' and (resid 91 through 99 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 9 )

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