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- PDB-8tuh: HLA B7:02 with RPIIRPATL -

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Basic information

Entry
Database: PDB / ID: 8tuh
TitleHLA B7:02 with RPIIRPATL
Components
  • ARG-PRO-ILE-ILE-ARG-PRO-ALA-THR-LEU
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-7 alpha chain
KeywordsIMMUNE SYSTEM / HLA-B7 HLA B7:02 MHC Influenza B nucleoprotein
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / secretory granule membrane ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / secretory granule membrane / 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 / lumenal side of endoplasmic reticulum membrane / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / defense response / 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 / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / 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 / Interferon alpha/beta signaling / 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 / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / 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 / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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. ...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 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
HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20010596362 Å
AuthorsLittler, D.R. / Rossjohn, J. / Chaurasia, P. / Petersen, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Nat Commun / Year: 2024
Title: CD8 + T-cell responses towards conserved influenza B virus epitopes across anatomical sites and age.
Authors: Menon, T. / Illing, P.T. / Chaurasia, P. / McQuilten, H.A. / Shepherd, C. / Rowntree, L.C. / Petersen, J. / Littler, D.R. / Khuu, G. / Huang, Z. / Allen, L.F. / Rockman, S. / Crowe, J. / ...Authors: Menon, T. / Illing, P.T. / Chaurasia, P. / McQuilten, H.A. / Shepherd, C. / Rowntree, L.C. / Petersen, J. / Littler, D.R. / Khuu, G. / Huang, Z. / Allen, L.F. / Rockman, S. / Crowe, J. / Flanagan, K.L. / Wakim, L.M. / Nguyen, T.H.O. / Mifsud, N.A. / Rossjohn, J. / Purcell, A.W. / van de Sandt, C.E. / Kedzierska, K.
History
DepositionAug 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-7 alpha chain
B: Beta-2-microglobulin
F: ARG-PRO-ILE-ILE-ARG-PRO-ALA-THR-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,41110
Polymers44,9773
Non-polymers4347
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint5 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.163, 57.163, 396.369
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

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Components

#1: Protein HLA class I histocompatibility antigen, B-7 alpha chain / MHC class I antigen B*7


Mass: 32059.129 Da / Num. of mol.: 1 / Fragment: UNP residues 25-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01889
#2: Protein Beta-2-microglobulin / 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide ARG-PRO-ILE-ILE-ARG-PRO-ALA-THR-LEU


Mass: 1038.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza B virus
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953651 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953651 Å / Relative weight: 1
ReflectionResolution: 2.2→48.5 Å / Num. obs: 21009 / % possible obs: 100 % / Redundancy: 21.1 % / Biso Wilson estimate: 35.9158930792 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.064 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1718 / CC1/2: 0.885 / Rpim(I) all: 0.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.20010596362→48.0288135138 Å / SU ML: 0.248252476543 / Cross valid method: FREE R-VALUE / σ(F): 1.34301427819 / Phase error: 21.0338737722
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245433386257 1029 4.93146745902 %
Rwork0.178652873375 19837 -
obs0.182001570887 20866 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.0896949816 Å2
Refinement stepCycle: LAST / Resolution: 2.20010596362→48.0288135138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 28 85 3284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006853892473113310
X-RAY DIFFRACTIONf_angle_d0.8580466144754484
X-RAY DIFFRACTIONf_chiral_restr0.053327849793451
X-RAY DIFFRACTIONf_plane_restr0.00540285557082594
X-RAY DIFFRACTIONf_dihedral_angle_d17.83976538681250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.31610.2570274837061440.1923875650732692X-RAY DIFFRACTION100
2.3161-2.46120.2632756943991460.2025034869482746X-RAY DIFFRACTION100
2.4612-2.65120.292304910671340.2066872789342782X-RAY DIFFRACTION100
2.6512-2.9180.286690062091280.2093980322082803X-RAY DIFFRACTION100
2.918-3.34010.2634785002921460.1889802623482820X-RAY DIFFRACTION100
3.3401-4.20780.2262843116491400.1554261918542887X-RAY DIFFRACTION100
4.2078-48.020.225192969671910.1678467368143107X-RAY DIFFRACTION100
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)
16.369312453890.380510743249-0.3486036316094.92303564757-0.35269659293.52969785524-0.0672512018366-0.4828369693610.1942839323680.121481398915-0.202048972946-0.332544376199-0.2173291668440.2783596654950.2410423537610.286253736051-0.04124558401150.0125271966420.2398851987560.04255741267940.172739002881-10.3931859311-3.83526661355-20.2361901784
28.698706949320.7472640371193.590593766473.91743116635-0.6424404870173.13512859996-0.03654089303430.39095456821.10855588706-0.0217488614157-0.241540304623-0.107516941159-0.3300298760640.02492732276720.2863343044850.354329320826-0.02723554950180.01276623372420.2368048078250.06193559921620.20606729089-14.24151170593.93209232904-28.4391713395
35.83295837011.45391383519-0.6462991791051.44607395653-0.052045840593.8074379613-0.155382159333-0.01873297687340.08541937616970.001832085998640.1369418808360.297391131698-0.1424608689-0.457580492596-0.004492103246790.282663896799-0.0286659554926-0.008934141575250.2161625473250.01486893971810.176879848005-24.5325605234-3.64029977889-27.4626811536
47.25587841761-4.63322554526-3.178082118235.324244652392.762083944393.451851025-0.3867511243461.04467500785-1.37758184769-0.333756714035-0.0283793655230.2400128250240.779108441395-0.0648898924140.230432672180.515570980089-0.0006218275320550.1111393487920.396883294843-0.1146179524530.453277596874-13.2009826205-16.1227854013-32.922489951
54.65645298716-0.1457317553190.7568611279361.60854302695-1.078039333124.5860057044-0.2135070558651.03768366594-0.262903857772-0.652299179373-0.0199336857501-0.2227133857390.324748072563-0.0394569670260.1763318323170.474226006407-0.07342712184630.07352846711840.28523109613-0.07251256737460.290635396983-15.6801854221-9.50585125648-37.1154988416
66.376565247335.41699629826-6.514579847175.42601596186-6.118424042657.482422653290.482880250341-1.024028795010.3377456929140.302160325296-0.4872663766580.0232018399843-0.203798613290.833789125810.1934366230570.4060649957860.0623682063140.05062889982140.3440151223660.06340430313120.376415936504-12.7335455886-30.2312816241-5.457678738
74.470256479721.67435033155-2.121488918495.0173432627-2.638175318724.66571001609-0.4766125758760.256898444946-0.419412695652-0.7847715343780.3611362394480.1152586525630.690842358226-0.1970742995330.0910928193840.384618460738-0.0292828890616-0.009834326221490.2002953972910.03197067754180.288239845095-18.1325493049-33.835929811-8.22050745018
82.083045988-2.243918769160.7859548347647.880210867163.647459364954.06001693620.09603322299170.64401027776-0.410284314175-1.88004437027-0.5312709225570.558577595697-0.650696331701-0.4530877291260.3170341031410.363496663149-0.1067817761740.04840954397310.8715894306440.1082097670350.397682435262-32.4040186749-9.60023144348-16.9820618854
94.04256749086-5.172460954393.267161201186.51791414986-4.434822833115.62110750553-0.352601611439-0.00496081002896-0.5972810575070.2724443073920.2852318359510.1421206412730.0913828501893-0.2735934369650.02062391061240.276074457662-0.06404697251550.02443477628510.1926777550960.02100072561830.306584092741-21.1821139434-17.6594102725-4.1345115788
104.640987284023.36566758419-0.5697713743774.834882152431.902299166142.27989437763-0.22156060802-0.694866789664-0.7305338753651.59651820445-0.295392899721-0.335316699156-0.03191000444571.169052820240.4297192223250.5462511517940.1432442518020.01147367905480.4993928308720.1292102882560.383404978085-9.35763906303-20.69810323966.22993123533
112.9642533457-1.66155704423.627204585751.36043125281-2.39608751239.26680430643-0.3103833277580.01311395728840.1638688459580.375270653998-0.0378729403496-0.128427711081-0.820628858510.06122515196620.3453235333590.345075306192-0.05197578334520.03497262127720.2413398138040.0393802600770.261922891867-20.8659938589-9.73676254917-4.92240186652
128.04849681063-1.24520523194-2.425057048055.41487232446-0.5723694826072.995650155050.942057612108-0.7473630960151.152595271040.370865793609-0.04874010609580.0106831160571-1.281919640580.443496142584-0.5889006777490.648638627265-0.0765798892135-0.03956600135870.3702005636450.02282750226550.315464328045-17.7476727826-4.434755353913.58705381733
134.417214411564.315567253444.963685754345.688434752144.077395848265.565530646950.384710961949-0.100819118243-0.0445276457340.4084970557370.01416722853550.1871630938560.703846354293-0.147105298388-0.398296530750.338038897925-0.02508181689180.02165427456250.3077900090550.03144106279950.279712563765-19.9483976042-11.2100856587-19.5785760079
144.30117776882-2.443758438754.110059643652.94406523954-2.811653098594.28090274507-0.213113107934-0.345104452841-0.1083341475930.4189773340490.0356033103409-0.0948759293456-0.5461754995380.07102456949860.2309130886450.243041495975-0.04023516421590.08479552113160.2506309831690.05781318358730.233130154028-15.4413926894-10.5447212132-4.09842229582
154.91944604914-3.630915821852.476084192564.05061412014-3.48748057523.90357707218-0.263930691202-1.88519717185-1.525006023441.308140116850.3688758232940.7639119485891.15069458834-0.704551696059-0.1533932317590.834992529712-0.0632221866420.02112419624650.5047021797620.08061291418580.52449155424-18.1601341399-17.28663445614.004349161
166.5042787921-3.620168521445.312126276093.71825568914-3.953494258214.85788674649-0.251186013457-0.6182985933540.05532529880720.2165652450710.4560988110070.345805410194-0.272295478753-0.608778420416-0.1937367036510.334063636280.03540420409880.03991808949310.3337512162610.001688674570240.237320114701-29.5758768881-7.82195149651-2.76075278888
176.43529300888-3.385421677134.476945790556.5430668479-1.253207485623.751244244510.943131258763-0.247277194763-2.174047453490.512226298473-0.4054269348920.830390374380.7340567708280.265547862369-0.2249814723840.380390343463-0.008424255483490.06958954914150.5104836543210.1296085907250.498926386404-23.0164131974-19.57539342573.83239096837
186.25329561404-1.624876797043.652558322943.80249397676-0.8738904535414.13768844951-0.08390730695411.125933497740.4440460152660.208606141677-0.1586837180910.003468609117740.5213221790560.26354562448-0.0002831459693530.460345007613-0.0651975774355-0.01185600355570.242890004176-0.0006766282059410.219990659811-12.9539198543-1.10762769486-33.6630159168
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 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 174 )
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 197 )
7X-RAY DIFFRACTION7chain 'A' and (resid 198 through 276 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 5 )
9X-RAY DIFFRACTION9chain 'B' and (resid 6 through 11 )
10X-RAY DIFFRACTION10chain 'B' and (resid 12 through 19 )
11X-RAY DIFFRACTION11chain 'B' and (resid 20 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 'F' and (resid 1 through 9 )

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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