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- PDB-3lko: Crystal Structure of HLA B*3501 in complex with influenza NP418 e... -

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Basic information

Entry
Database: PDB / ID: 3lko
TitleCrystal Structure of HLA B*3501 in complex with influenza NP418 epitope from 1934 strain
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-35 alpha chain
  • NP418 epitope from 1934 influenza strain
KeywordsIMMUNE SYSTEM / HLA B*3501 / NP418 epitope / influenza / swine-flu / T cell immunity / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Amyloid / Amyloidosis / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted
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 / 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 / detection of bacterium / 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 / 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 / detection of bacterium / secretory granule membrane / 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 / lumenal side of endoplasmic reticulum membrane / 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 / defense response / 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 / Interferon alpha/beta signaling / 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 / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / 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, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsGras, S. / Kedzierski, L. / Valkenburg, S.A. / Liu, Y.C. / Denholm, J. / Richards, M. / Rimmelzwaan, G.F. / Doherty, P.C. / Turner, S.J. / Rossjohn, J. / Kedzierska, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Cross-reactive CD8+ T-cell immunity between the pandemic H1N1-2009 and H1N1-1918 influenza A viruses.
Authors: Gras, S. / Kedzierski, L. / Valkenburg, S.A. / Laurie, K. / Liu, Y.C. / Denholm, J.T. / Richards, M.J. / Rimmelzwaan, G.F. / Kelso, A. / Doherty, P.C. / Turner, S.J. / Rossjohn, J. / Kedzierska, K.
History
DepositionJan 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 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: HLA class I histocompatibility antigen, B-35 alpha chain
B: Beta-2-microglobulin
C: NP418 epitope from 1934 influenza strain


Theoretical massNumber of molelcules
Total (without water)44,9143
Polymers44,9143
Non-polymers00
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-25 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.990, 81.910, 110.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, B-35 alpha chain / MHC class I antigen B*35


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, HLAB / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


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 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide NP418 epitope from 1934 influenza strain


Mass: 1094.305 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15-25% PEG 4000, 0.2M NH4Acetate, 0.1M Na-Citrate, pH 5.6, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→65.82 Å / Num. obs: 43699 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.376 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.28
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.90.4075.4556536476100
1.9-20.2698.7449435224100
2-2.10.20311.6370344298100
2.1-2.20.17314304413532100
2.2-2.30.14416.4255112969100
2.3-2.40.1318.3214432489100
2.4-2.50.11620.3180452107100
2.5-30.08925587086903100
3-3.50.06432.829328352099.9
3.5-40.05637161841997100
4-50.04839.6161412011100
5-60.04938.97345904100
6-100.04538.680491011100
100.04239.1186225884

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.5.0088refinement
PDB_EXTRACT3.005data extraction
BueIcedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2FYY

2fyy


Resolution: 1.8→65.82 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.191 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2196 5 %RANDOM
Rwork0.198 ---
obs0.2 43699 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 43.36 Å2 / Biso mean: 22.069 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.96 Å2-0 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→65.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 0 254 3421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213349
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9374566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0935401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.80423.169183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14815547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2581534
X-RAY DIFFRACTIONr_chiral_restr0.0930.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212689
X-RAY DIFFRACTIONr_mcbond_it0.6611.51984
X-RAY DIFFRACTIONr_mcangle_it1.16823225
X-RAY DIFFRACTIONr_scbond_it1.89431365
X-RAY DIFFRACTIONr_scangle_it2.9484.51341
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 132 -
Rwork0.312 3064 -
all-3196 -
obs--99.97 %
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)
12.2805-1.2647-0.31031.84020.34480.43620.07960.06730.1974-0.1026-0.0292-0.0977-0.03320.0318-0.05040.072-0.00410.01030.05360.02190.02699.5304-5.4315-29.9281
25.5122-0.7384-2.17661.324-0.02881.63690.1790.4590.1606-0.3591-0.16330.1761-0.1005-0.0679-0.01570.14410.0152-0.04930.09780.00870.06220.2414-6.7358-35.0483
32.0537-1.4795-0.51523.58260.57620.5354-0.03230.0866-0.3336-0.0722-0.04270.42180.033-0.01940.07490.03970.0023-0.01660.0249-0.00530.0891-1.4315-18.8997-26.0251
40.5446-0.16030.05351.19540.39220.6058-0.04380.04770.0021-0.04680.0263-0.06970.03960.12550.01750.02440.00890.00410.0375-0.00020.020319.466-16.6018-20.8539
51.2067-0.44681.99371.1418-1.65667.21370.1112-0.1766-0.0080.0380.0627-0.13640.5372-0.1263-0.17390.10210.0193-0.0650.0722-0.01720.053825.1062-17.1559-1.9316
67.54291.75380.18542.3306-0.01191.1556-0.2292-0.28450.24850.20080.0815-0.1967-0.0331-0.00380.14770.08650.0312-0.05610.0554-0.03280.061417.3215-1.4231-9.8071
76.06152.23751.55731.42820.56351.4399-0.2532-0.17950.49230.03930.07690.0363-0.1176-0.06850.17620.10760.0266-0.04990.0608-0.03830.097713.75023.2808-12.8799
83.98032.80960.80113.22972.79980.6492-0.21780.13060.528-0.7620.1561-0.0869-0.2480.02190.06180.2160.0118-0.08250.02720.02160.234517.004411.5782-17.2479
93.22551.12350.52662.14320.44151.2339-0.0695-0.20630.24360.14020.0654-0.2151-0.06480.0190.00410.0610.0353-0.04530.0521-0.0360.077713.92741.4697-12.8546
100.5461-0.59541.50292.41631.43439.8065-0.2103-0.18510.08520.4880.118-0.0866-0.1827-0.28620.09230.21190.0095-0.07720.4784-0.22180.194116.12224.0008-2.7941
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 52
2X-RAY DIFFRACTION2A53 - 88
3X-RAY DIFFRACTION3A89 - 147
4X-RAY DIFFRACTION4A148 - 211
5X-RAY DIFFRACTION5A212 - 276
6X-RAY DIFFRACTION6B0 - 19
7X-RAY DIFFRACTION7B20 - 43
8X-RAY DIFFRACTION8B44 - 51
9X-RAY DIFFRACTION9B52 - 88
10X-RAY DIFFRACTION10B89 - 99

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