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- PDB-8emi: Crystal structure of a HLA-B*35:01-NP8 epitope from 2005 H1N1 inf... -

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Basic information

Entry
Database: PDB / ID: 8emi
TitleCrystal structure of a HLA-B*35:01-NP8 epitope from 2005 H1N1 influenza strain
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Nucleoprotein NP8 epitope
KeywordsIMMUNE SYSTEM / HLA B*3501 / NP418 epitope / T cell immunity / glycoprotein / host-virus interaction / immune response
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
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, 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
ACETATE ION / MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57301511861 Å
AuthorsLittler, D.R. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: Molecular determinants of cross-strain influenza A virus recognition by T-cell receptors
Authors: Quinones-Parra, S. / Littler, D.R. / Rossjohn, J. / Kedzierska, K.
History
DepositionSep 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Nucleoprotein NP8 epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9745
Polymers44,8563
Non-polymers1182
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-22 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.869, 81.528, 109.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein MHC class I antigen


Mass: 31940.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Details (production host): PET-30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4NBT2
#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 / Plasmid: PET-30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide Nucleoprotein NP8 epitope / Nucleocapsid protein / Protein N


Mass: 1036.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus (strain A/2005/H1N1)
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4 / 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: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.57→37.3 Å / Num. obs: 63452 / % possible obs: 99 % / Redundancy: 2 % / Biso Wilson estimate: 17.4671780787 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.042 / Net I/σ(I): 20.9
Reflection shellResolution: 1.57→1.63 Å / Mean I/σ(I) obs: 2.82 / Num. unique obs: 6187 / CC1/2: 0.854 / Rrim(I) all: 0.394

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LKS

3lks


Resolution: 1.57301511861→37.2283178519 Å / SU ML: 0.15412053064 / Cross valid method: FREE R-VALUE / σ(F): 1.35665517843 / Phase error: 20.802747564
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.207687528264 3233 5.09575222634 %
Rwork0.175811318544 60212 -
obs0.177453306722 63445 99.3579202882 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.855464759 Å2
Refinement stepCycle: LAST / Resolution: 1.57301511861→37.2283178519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 8 512 3675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01383947506193313
X-RAY DIFFRACTIONf_angle_d1.495458724874512
X-RAY DIFFRACTIONf_chiral_restr0.0822127327512462
X-RAY DIFFRACTIONf_plane_restr0.0100898137321600
X-RAY DIFFRACTIONf_dihedral_angle_d17.51559779791241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.59650.2974304114371340.2482103777412508X-RAY DIFFRACTION96.8120190546
1.5965-1.62140.2691830557661600.2310999403822562X-RAY DIFFRACTION99.780058651
1.6214-1.6480.22806708411370.2241629514232549X-RAY DIFFRACTION97.6727272727
1.648-1.67640.2550646241311370.2124249152272587X-RAY DIFFRACTION99.9633027523
1.6764-1.70690.2246416412421450.2029882602372560X-RAY DIFFRACTION98.0427691192
1.7069-1.73980.2283952160431350.2040274645842597X-RAY DIFFRACTION99.8538011696
1.7398-1.77530.2548606010021400.2042843477652572X-RAY DIFFRACTION98.510715583
1.7753-1.81390.2379145524151440.2054149264992586X-RAY DIFFRACTION99.1645477661
1.8139-1.85610.2851155214151270.2114786618412599X-RAY DIFFRACTION99.561723886
1.8561-1.90250.2164850659791400.1996861949692554X-RAY DIFFRACTION99.0441176471
1.9025-1.95390.1920590985641490.185226147152622X-RAY DIFFRACTION99.533045977
1.9539-2.01140.226625730581420.1813918459442594X-RAY DIFFRACTION99.7084548105
2.0114-2.07630.2082730429811160.1784746766712630X-RAY DIFFRACTION99.4207096307
2.0763-2.15050.2255525772171430.175283076112618X-RAY DIFFRACTION99.6391194515
2.1505-2.23660.2245855869091390.1741792385852636X-RAY DIFFRACTION99.6767241379
2.2366-2.33840.2031633400591560.1731043914862602X-RAY DIFFRACTION99.7829232996
2.3384-2.46170.2082090952151540.174883748792625X-RAY DIFFRACTION99.9280834232
2.4617-2.61580.2024481411171440.1700121651572631X-RAY DIFFRACTION99.8920086393
2.6158-2.81780.2199144522031340.1770457907442674X-RAY DIFFRACTION100
2.8178-3.10120.2180689330831160.1729108133332699X-RAY DIFFRACTION99.9644886364
3.1012-3.54960.1904101406331410.165030627172678X-RAY DIFFRACTION99.9645390071
3.5496-4.4710.166162036581570.1493218794982690X-RAY DIFFRACTION99.9297999298
4.471-37.20.1930053031811430.165056054732839X-RAY DIFFRACTION99.3668777074
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)
11.42200731606-0.494041258219-0.2500030551911.20786225652-0.01403063151010.2432653996070.0403411219620.124818449098-0.0883431314751-0.130936903071-0.03927115681410.1388871125720.01773763545790.00159815112323-0.001565704771620.09545507796080.00856025757295-0.0200854113940.086067196983-0.001087893006010.055007781807329.408598227768.640792349278.6424504444
20.3466051864520.1134868767740.645777616310.186742779977-0.3684420806050.7116026346970.00334795051648-0.07141568541580.03272361198190.07609262528030.0151515102613-0.1005634104480.114628748572-0.03989554861950.001186623684980.1861145746090.0273690612551-0.03500690208910.1834475008680.01143883227350.13732286905251.340250772766.1390215167105.605354455
30.00850213975089-0.02586115451930.007876852069620.12806089926-0.0847236516910.0553237507532-0.06436396992270.01758509947470.08720311803710.2859255002160.0488469305922-0.0847241676479-0.0497323594928-0.00945469428386-1.59743192866E-70.2256702155330.0360255176079-0.01447464923520.186445788067-0.0248657266250.1468781069434.750906708178.0872326068100.342369029
40.0117660252005-0.0412178525665-0.01243935999730.1497870975490.05315933342840.02601787270360.0215860226040.06888668772020.1208479045990.0235309612981-0.028634857064-0.264501936084-0.121943210440.120991126202-0.00146101779210.220170759181-0.025084591867-0.127956700990.291609251658-0.06520570603210.41214138196357.650994472683.761611960598.894540084
50.01822588565370.0085809885927-0.0039647973380.051398494657-0.1426844041050.236069485389-0.272942991403-0.1515676020530.2520695016770.0674600694310.0779569039383-0.0983114092561-0.125811584042-0.000572345357646-0.00109604212390.2096226406750.00744728016345-0.0698972000920.165707346854-0.02740894995210.21065553961438.72228749684.01531435295.967069545
60.004129428204-0.00199155010930.003459449784730.006494410452090.004570881916110.01274765759420.1589862376050.02726399522380.1064359875690.13875580047-0.01049893613540.0472655677057-0.0755590060745-0.01116863606224.05245870834E-50.325956699768-0.00317427477775-0.1146821809560.221220506433-0.08671991708420.46146996853142.892975955196.821294332399.4329238966
70.001980256137130.00442334331662-0.0004104516127810.01529170716120.000636270950967-0.001919248849280.001636649531460.1453835242090.0934990299373-0.0627337919815-0.0195254413374-0.0498835677547-0.175401972291-0.003209725578953.44780224879E-50.298059525865-0.0195829299133-0.06537939367850.1760465293460.03997812042150.31086708997542.812011113890.840450733488.8100620867
80.120698159086-0.1419266109840.01496536504530.1083633570060.01559212841730.127475712803-0.0147826582262-0.05804032733940.07116790539170.120616381531-0.00969807593249-0.1659719771750.006756773205630.042622782023-3.33242613868E-70.1312771741720.00580113652466-0.02788048731190.133699860020.008135731292910.1557679522338.462493371578.273858287991.4450635474
90.00223011735356-0.005753851930160.0007598865712080.002047182449840.003319249579110.003621860826950.0512653468885-0.0699908473830.01605299067290.0236863231995-0.0320252241273-0.0198215117529-0.0108129937639-0.002786638817451.45682690391E-50.457144440691-0.0205053422446-0.1690609462030.364657976816-0.1064564892040.57664971072853.558589799193.1877514998106.43009545
100.01734274431010.006383091528120.03818819834840.0197165863826-0.01320450871660.045647073662-0.161382620568-0.2657117723640.2312857654440.506195545970.0489686475409-0.117762945158-0.121050517101-0.0897893140698-0.00011015769540.3051099106270.0527149314841-0.05228699318640.23205318087-0.09896451619940.28520324716132.618853637387.5037212699102.009673574
110.04186404281960.0228774754553-0.06790529907830.075618045483-0.04930803168970.1190683327930.00266832111602-0.188830979137-0.03633173495240.222420856069-0.0986421142911-0.128372297919-0.03976818866620.134622015256-0.1278998919910.3942697670110.0486264128952-0.1641751030420.308587322687-0.09925390460030.26070833261845.523495436383.894717267106.823097045
120.00620931403023-0.0008160124426140.00473219686335-0.01108279954560.015876817703-0.00629699055741-0.02829399059660.174237789040.039385322834-0.1587629773160.007932089946250.2346377594120.000100079299091-0.03926167004866.72553303882E-60.194962130342-0.00605811521681-0.02809143867130.230639715057-0.01405160410790.20513286238325.46863558167.232670842372.828661831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 276 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 11 )
4X-RAY DIFFRACTION4chain 'B' and (resid 12 through 19 )
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 41 )
6X-RAY DIFFRACTION6chain 'B' and (resid 42 through 46 )
7X-RAY DIFFRACTION7chain 'B' and (resid 47 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 71 )
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 77 )
10X-RAY DIFFRACTION10chain 'B' and (resid 78 through 90 )
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 99 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 9 )

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