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- PDB-8emj: Crystal structure of HLA-B*35:01-NP9 epitope from 2006 H1N1 influ... -

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Basic information

Entry
Database: PDB / ID: 8emj
TitleCrystal structure of HLA-B*35:01-NP9 epitope from 2006 H1N1 influenza strain
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Nucleoprotein NP9 epitope
KeywordsIMMUNE SYSTEM / HLA B*3501 / NP418 epitope / T cell immunity / glycoprotein / host-virus interaction / immune response
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...antigen processing and presentation of peptide antigen via MHC class I / 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 / 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 / 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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75002880736 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 NP9 epitope


Theoretical massNumber of molelcules
Total (without water)44,8403
Polymers44,8403
Non-polymers00
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-27 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.919, 81.737, 109.417
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 / Variant: 3501 / Plasmid: PET-20 / 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 NP9 epitope / Nucleocapsid protein / Protein N


Mass: 1020.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus (strain A/2006/H1N1)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: PEG, Acetate

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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 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→24.8 Å / Num. obs: 46767 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 16.9172395997 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.042 / Net I/σ(I): 17.8
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4567 / CC1/2: 0.888 / Rrim(I) all: 0.326

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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: 1.75002880736→24.797072884 Å / SU ML: 0.189764561939 / Cross valid method: FREE R-VALUE / σ(F): 1.35597307965 / Phase error: 21.2686681205
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.213573953668 2341 5.00673695917 %
Rwork0.171749861358 44416 -
obs0.173853733974 46757 99.8846424986 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.9992744442 Å2
Refinement stepCycle: LAST / Resolution: 1.75002880736→24.797072884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 0 463 3625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01347926767463279
X-RAY DIFFRACTIONf_angle_d1.519253084694461
X-RAY DIFFRACTIONf_chiral_restr0.114395975595457
X-RAY DIFFRACTIONf_plane_restr0.0100539489728590
X-RAY DIFFRACTIONf_dihedral_angle_d19.0931114761228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.751-1.78570.3060640846651180.2452233711162537X-RAY DIFFRACTION98.7723214286
1.7857-1.82460.2402315209891100.2254656217192614X-RAY DIFFRACTION99.9633027523
1.8246-1.8670.278925604871170.2140729589952579X-RAY DIFFRACTION99.9629217649
1.867-1.91370.2305201717121300.2030275893192599X-RAY DIFFRACTION99.9633699634
1.9137-1.96540.2782802685741490.1935454658612578X-RAY DIFFRACTION99.9633431085
1.9654-2.02320.2682325795391620.1809198128792549X-RAY DIFFRACTION99.8894620486
2.0232-2.08850.2394952366011390.1860491097362583X-RAY DIFFRACTION99.9265785609
2.0885-2.16310.2352102788071430.1827886261672575X-RAY DIFFRACTION100
2.1631-2.24960.2270805608521200.1800818444832618X-RAY DIFFRACTION99.9634903249
2.2496-2.35190.217923051131390.1718458128692601X-RAY DIFFRACTION99.9635169646
2.3519-2.47580.2475576560251440.1749325943112600X-RAY DIFFRACTION100
2.4758-2.63080.2102152283851330.1724780543042617X-RAY DIFFRACTION100
2.6308-2.83360.2371532882041340.1749194481742632X-RAY DIFFRACTION99.9638597759
2.8336-3.11830.2393142318351600.1690297298352609X-RAY DIFFRACTION99.963898917
3.1183-3.56840.1817601865391450.1593373711022651X-RAY DIFFRACTION100
3.5684-4.49140.1611027322631330.1389478001512678X-RAY DIFFRACTION99.8579040853
4.4914-24.70.1685171191671650.1610200466792796X-RAY DIFFRACTION99.9325008437
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)
10.0779821300598-0.08685117480470.01639586077740.0927572520786-0.02445307065570.1226087098340.0611665678181-0.06577824640620.09617423486150.0492483023362-0.04112639298040.0169988667049-0.0336940882757-0.04272115510370.03524601805150.079079464513-0.01765883936270.01732414849590.0807110216613-0.02365552424430.0761113356685-10.239829765-5.695248986830.4999894843
20.2421796086470.00839258123037-0.07138081349450.791897902473-0.1998935141060.2429381883240.0191289354024-0.111520719823-0.009128133595370.224806726766-0.128961682603-0.2086302756570.0188913530111-0.0460494902829-0.1822955883790.131886135935-0.0359512349904-0.03517029908230.136572191705-0.03667100780890.02896416693190.15207109816-6.6581847202336.256558315
30.0907175982624-0.128785419249-0.04896536257970.1468685383410.05732602571740.0424502605929-0.04210441721630.0525179347363-0.109726951323-0.01322236262650.0333696177562-0.09948253189370.07124433227430.000158915393686-0.0002332858367010.0684661571683-0.01145193240450.00447736633730.04948928901840.007876711886170.0935689091273-1.79864552587-16.075032899325.4592637935
40.3225343277120.39456149374-0.07999000136310.515029018971-0.05336461391530.1876255936450.00642021959874-0.0499440889399-0.2402649484610.0900283529295-0.0267125967631-0.302434184360.0834515486044-0.008300820615550.01410878207830.07364282443450.00152452165433-0.01726881380860.05841677863660.04397457342190.12182010544-1.01809840474-21.377410997931.5438557716
50.1366454007370.05687147922160.1346048897680.135749087846-0.05852959995540.2197763656420.06907680445080.0387006860747-0.0147186813681-0.1329156553460.1531001003230.1669352236440.1839177564360.07129467095360.2527698843220.1663799314-0.0192809085096-0.06303352873310.148176828881-0.01531821393860.0865842649676-25.6159298988-15.14755032954.53029311522
60.06305483222850.01006357610660.08132361136120.07672133687690.01609615662750.1060269787620.06118492691950.0461528208505-0.0381275705166-0.04020134303490.08417554523560.1276568194080.272891344246-0.05894995429250.1656606268530.0995873857669-0.0755771713748-0.1882087055860.133422452728-0.0430271521964-0.0622380808454-26.6133152077-15.59846456213.24176694061
70.02939452941930.04509590896110.01709608825780.1704599218870.02438651243860.0114589425162-0.06392056428140.01357978931970.0367346084524-0.14391439750.01495628398590.07079040604990.008626327222820.02545922096130.004188160108710.15072946409-0.01561381620960.00541691099880.1622800762050.007210523161880.0850706203076-7.85757865945-3.795872144259.4351359358
80.004593237303880.00404082835524-0.002576374675230.00513535539619-0.004752883074680.003836262796260.007180085326540.00909801585770.0272139525221-0.0210241728808-0.02625092116010.0629297346849-0.031570986458-0.06107695220250.001973994239140.1514934591840.0165535626455-0.09181431515840.2374164324010.02280725764950.280153137459-32.47528320812.4789204858310.4042788446
90.0369451396429-0.0218767002922-0.007057486892530.01786414938280.02293609259290.0707450933154-0.1575152965580.03658026433510.126194378837-0.09562029141430.06419472237390.134202867019-0.1001243178350.00139323526815-0.005649209777120.112270215901-0.00148532917521-0.04688330941410.08528747109830.01056581380190.134123302128-13.3451766842.486949381713.4115193767
100.00124550343177-0.002898598931460.0004838653029520.006701018089320.000419051911306-0.000344553800151-0.0597654454140.001768658652260.132829567482-0.012088663003-0.02887604225250.0738845708174-0.05265242468790.0008612961665385.92519634647E-60.232259429290.0289633000272-0.07673001103930.101928872994-0.01044351473140.264760503943-17.566981868412.187212992915.4575641222
110.06086447849540.0554359428777-0.01755109932950.0476019869138-0.01247647171540.02259125548540.0121530151320.005718409310740.0524005412327-0.0698761215861-0.02163778641360.1969008446980.00458305888996-0.00516494356417-0.008324262452760.0845608246901-0.00321116112056-0.02207438801210.0883842160592-0.01648128189840.105349078834-13.0665284632-3.1906919777817.9424514249
120.0125994447765-0.00418347628346-0.002691194141560.01566668862510.01515098803670.0297036005219-0.04123982076560.09305049324260.0954149029351-0.1833274127590.003385992100050.105529787207-0.0846127530061-0.00376791255363-0.02332793669710.211197276438-0.0250721297559-0.06288862358580.1692692407020.07596139771790.202192060182-13.96095124327.71196530175.86163795348
130.0033539677753-0.00133837645840.004587594617450.000710292936829-0.003224214759470.0113866993360.02906787616250.0210001425705-0.0121273476002-0.08469860447080.003064109291720.01104276135790.00534264337915-0.002403103943820.002469656040390.270410186092-0.0563452269388-0.1283315105860.2396667885570.08052753256890.228999905013-20.09630666712.410498293282.49144705027
140.005319243511670.0002694436153140.000992653351616-0.0004589045167340.001328312241730.00104913929354-0.0100193610622-0.0266495834234-0.008996528116930.0326722005527-0.0303024709484-0.08160829975590.000175505555511-0.02086979620157.46707447164E-60.128242034327-0.0124931786361-0.01206187449530.1552774488930.03267756349740.137185640107-0.0141346861789-14.344769151236.8444369708
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 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 174 )
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 227 )
6X-RAY DIFFRACTION6chain 'A' and (resid 228 through 276 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 11 )
8X-RAY DIFFRACTION8chain 'B' and (resid 12 through 19 )
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 41 )
10X-RAY DIFFRACTION10chain 'B' and (resid 42 through 51 )
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 90 )
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 99 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 9 )

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