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- PDB-8emf: Crystal structure of a HLA-B*35:01-NP6 epitope from 1977 H1N1 inf... -

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Basic information

Entry
Database: PDB / ID: 8emf
TitleCrystal structure of a HLA-B*35:01-NP6 epitope from 1977 H1N1 influenza strain
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Nucleoprotein NP6 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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.80482421415 Å
AuthorsLittler, D.R. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Sci Immunol / Year: 2025
Title: Molecular determinants of cross-strain influenza A virus recognition by alpha beta T cell receptors.
Authors: Quinones-Parra, S.M. / Gras, S. / Nguyen, T.H.O. / Farenc, C. / Szeto, C. / Rowntree, L.C. / Chaurasia, P. / Sant, S. / Boon, A.C.M. / Jayasinghe, D. / Rimmelzwaan, G.F. / Petersen, J. / ...Authors: Quinones-Parra, S.M. / Gras, S. / Nguyen, T.H.O. / Farenc, C. / Szeto, C. / Rowntree, L.C. / Chaurasia, P. / Sant, S. / Boon, A.C.M. / Jayasinghe, D. / Rimmelzwaan, G.F. / Petersen, J. / Doherty, P.C. / Uldrich, A.P. / 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 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Oct 8, 2025Group: 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

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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 NP6 epitope


Theoretical massNumber of molelcules
Total (without water)44,8583
Polymers44,8583
Non-polymers00
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-24 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.000, 81.645, 109.239
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: B35*01 / Plasmid: PLASMID / Details (production host): PET30 / 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: PLASMID / Details (production host): PET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide Nucleoprotein NP6 epitope / Nucleocapsid protein / Protein N


Mass: 1038.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus (strain A/1977/H1N1)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 51.48 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→25.9 Å / Num. obs: 42596 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 18.1173206963 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.037 / Net I/σ(I): 19.6
Reflection shellResolution: 1.81→1.87 Å / Num. unique obs: 4086 / CC1/2: 0.898 / Rrim(I) all: 0.31 / % possible all: 97

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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: 1.80482421415→25.8992726523 Å / SU ML: 0.1811965619 / Cross valid method: FREE R-VALUE / σ(F): 1.35856944734 / Phase error: 19.8583684912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.203165366562 2148 5.04379270669 %
Rwork0.178800196108 40439 -
obs0.180050003169 42587 99.6840035579 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.724710139 Å2
Refinement stepCycle: LAST / Resolution: 1.80482421415→25.8992726523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 0 450 3613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01069605568493262
X-RAY DIFFRACTIONf_angle_d1.502145732954433
X-RAY DIFFRACTIONf_chiral_restr0.10564570197453
X-RAY DIFFRACTIONf_plane_restr0.00767238145013585
X-RAY DIFFRACTIONf_dihedral_angle_d18.779375151222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.84680.2754599319131360.2676531412062571X-RAY DIFFRACTION95.7891012031
1.8468-1.8930.2679599670391380.2280159973132672X-RAY DIFFRACTION99.9644254714
1.893-1.94410.2350844884011420.2141374175122652X-RAY DIFFRACTION99.9284692418
1.9441-2.00130.2363682311721500.1995125474142637X-RAY DIFFRACTION99.9641319943
2.0013-2.06590.2276727669811220.1942008696632697X-RAY DIFFRACTION99.9291031549
2.0659-2.13970.2101153099281420.1964133924212677X-RAY DIFFRACTION99.9645390071
2.1397-2.22530.1993456303031480.1856720107542658X-RAY DIFFRACTION99.9287749288
2.2253-2.32650.2031900874441380.1846226802852694X-RAY DIFFRACTION99.9294283698
2.3265-2.44910.2079812533861260.1826247206252693X-RAY DIFFRACTION100
2.4491-2.60240.2216917643151780.1852416659782669X-RAY DIFFRACTION100
2.6024-2.80310.2473675372441470.1914489003632706X-RAY DIFFRACTION100
2.8031-3.08480.2460985324381390.1805112769822709X-RAY DIFFRACTION100
3.0848-3.53020.2097484931571480.1644258835522728X-RAY DIFFRACTION99.9305072967
3.5302-4.44410.153709565451550.1470625529162754X-RAY DIFFRACTION100
4.4441-25.80.1484171102661390.1622199219282922X-RAY DIFFRACTION99.934704538
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)
12.443681532390.797433668556-0.5660548288721.34287237064-0.402953008190.6110013095480.118608457276-0.125214447760.2983095385240.131292107781-0.04257696361390.202925347983-0.0653824519978-0.0380819974569-0.06274675372650.109194846505-0.003502978348760.02204783631410.105992017204-0.02529187354520.0799301886035-10.3562086314-5.6003068955530.3723063794
23.40669556738-0.362769298021-1.761846357071.512860330430.6272806748712.205490029570.207351079441-0.4871441845270.1417994698650.607124464293-0.284307967432-0.530236924087-0.235559091850.120791861368-0.1150853343970.193183043862-0.0350222570474-0.022539670170.15151727792-0.0453749088285-0.01744449078990.115982272267-6.5115185483836.1224785372
33.465650940440.566604839809-1.137565926472.46613298366-0.1484537789141.29535230102-0.145479204190.0172221200907-0.316939983625-0.03428603817640.0546252412532-0.1429385240940.158724580214-0.0400196750490.03434140654040.08275534407940.00332919079579-0.02540421547470.0654649078650.003000416174780.0417592607333-1.76188129172-15.864427280225.2769528058
41.713866635710.502537732912-0.3044030582161.70585982818-0.1334518368970.61934685754-0.0252618099887-0.20702454045-0.369395796960.184455559444-0.0490553198477-0.36911215710.06767997467620.03990807118520.05624456465610.1315166031260.00180360988392-0.0400674103180.1049548506050.03173765099840.1516595626-0.999851688162-21.229126301531.4197002407
50.737672066552-0.02282420828921.252292207050.921391849614-0.2594944004112.966379585110.03788800133210.1201249710830.0174190539282-0.2307005773190.1467353819370.1594962430810.261696901362-0.0797408353254-0.04123830614990.138143529988-0.0259471674732-0.03512259460850.137732130399-0.002103577226150.121430534151-26.7179379697-13.71571069566.22540947696
61.199399453430.09428059699951.433565901041.363679858720.5945932706673.477655830720.1414203190850.244425920725-0.125055033366-0.1857956512320.05417934202210.155458220380.501344924790.0280567603903-0.1056083075330.21390739254-0.0301051608888-0.07722627426810.168054777334-0.007711257605640.146157506923-25.6151880635-16.6460954572.0068356122
72.705402407770.4870171134682.519800534313.234417182071.717274245342.87985244271-0.1220940845590.344149804262-0.116419195449-0.1580227014290.375644866203-0.3384375353230.1003308562390.197896516381-0.2081281841970.191541948652-0.0123473728760.05638799524250.2646131667420.0487117690530.1094849520051.42797959482-5.338823576610.3287282855
87.111853317291.1563393416-1.895319627570.7158275969620.3368842151673.13426442862-0.03095391293610.1275464094330.126163982303-0.2593399827060.02625586968230.0992814403207-0.0266220023845-0.02857006503480.01979890442490.168463189642-0.0239270852682-0.05190404204730.1162267027030.01410548754840.108949840294-17.3026902153-2.111306641398.29546936837
91.29935173665-1.961876049881.449885330743.0612079803-2.21793522372.01390000002-0.03411989140740.03563204146440.265003816544-0.2007163941290.1334885429560.805872933523-0.136457443187-0.693846352387-0.1415656480140.1848101805250.0401915039452-0.100819487180.3287737385970.03776758126450.380999957999-32.54232208732.4551627754310.2854270525
101.96896598477-0.6068405201940.1670091195021.261265231540.1969942571251.18877719302-0.2856629663350.06448534310510.275150634046-0.04348774073840.1363617898630.164075268332-0.181995549194-0.004775779972370.1366824431120.143059033628-0.0173353327671-0.05445851337360.09240217686330.01579010096790.155554530953-13.37675241862.5393052414313.3112136189
113.02675997555-1.73553707021-0.05996458615011.87502395335-0.8397841766142.34321932074-0.133057033484-0.2084701946690.8401250854340.276698865606-0.09362018264610.11283521525-1.021165192380.1531036154540.1672213971650.3573572782460.0042612898532-0.1177331132460.141869652778-0.01595643291260.355431557218-17.551910173712.248640662415.2735178097
123.5310879568-1.387837678961.057709512782.04244008236-0.8525292991751.4531189371-0.06394736476540.0210142434797-0.0841178644032-0.058603995360.05810308786880.452687422928-0.0876445836582-0.05316976512930.006765827443190.0837098783603-0.0205294536841-0.02891709789370.0902593910833-0.0165949069980.0968874003297-13.0696803191-3.1274130985117.8376528421
135.29194740773-2.014708347570.6234437287241.32100306802-0.161081376031.36568109893-0.046884861420.3438007385590.664976648041-0.0831300345798-0.02656082502670.203180678574-0.340022874527-0.1961927831460.06730150281630.298980464382-0.00963580584882-0.1291549082370.2387063778380.1191903431090.380168217842-20.85439612759.623509257095.25759136297
145.87544477016-2.164358083830.09297999219737.495141201920.005488818434451.7943044499-0.1382850303531.452429243020.29060713011-0.865801960597-0.174468878752-0.470029843126-0.08566903082180.3890895525060.3502417071470.247498100734-0.08428906937290.01818540180820.3047044817820.09655106757720.225551984212-1.421673073194.265956329366.50681007994
155.979463634040.6167323219191.529910553181.515576733160.2489040242971.689027256560.0889411866620.736021570945-0.0347289871561-0.4723608017040.121057180992-0.0723844408386-0.0568292450283-0.0120855506367-0.1545888569710.369392111489-0.0618262642965-0.124956126710.2743414964660.105487698710.191335858623-20.15406793782.35560198122.36997801966
162.685962524070.502387434215-2.099800206172.28058584086-0.4914811681.692585586550.156600200599-0.6616485191070.07603641108720.310327865677-0.159773613607-0.4477456655280.01107892720720.3180708271680.0578314401060.215239613462-0.0208991651721-0.02491834389930.208907262570.04605855056240.140462456439-0.146052807835-14.253544166736.914342618
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 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 276 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 5 )
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 11 )
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 19 )
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 41 )
11X-RAY DIFFRACTION11chain 'B' and (resid 42 through 51 )
12X-RAY DIFFRACTION12chain 'B' and (resid 52 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 83 )
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 99 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 9 )

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