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

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Basic information

Entry
Database: PDB / ID: 3lkq
TitleCrystal Structure of HLA B*3501 in complex with influenza NP418 epitope from 1977 strain
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-35 alpha chain
  • NP418 epitope from 1977 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 / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding ...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 / 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 / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / 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 / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / signaling receptor binding / focal adhesion / 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 / 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 / Immunoglobulins / Immunoglobulin-like fold / 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

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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 1977 influenza strain


Theoretical massNumber of molelcules
Total (without water)44,8863
Polymers44,8863
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-25 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.330, 81.990, 110.420
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 1977 influenza strain


Mass: 1066.291 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.48 %
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→65.83 Å / Num. obs: 43813 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.641 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.57
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.90.5543.432260652699.9
1.9-20.328625845520999.9
2-2.10.2318.321462432999.9
2.1-2.20.17610.617614356299.9
2.2-2.30.1412.814736297799.8
2.3-2.40.1214.712446250599.9
2.4-2.50.10117104772122100
2.5-2.60.08519.39020182699.8
2.6-2.70.07920.67644156399.8
2.7-30.062517286353299.6
3-40.03835.426334552199.4
4-50.02943.89406199798.9
5-60.02843.2429889998.5
6-100.02643463699398
100.02245.1107725281.6

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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→65.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.119 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2207 5 %RANDOM
Rwork0.198 ---
obs0.199 43813 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 44.95 Å2 / Biso mean: 22.596 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å20 Å2
2---0.96 Å2-0 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→65.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 0 260 3425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213455
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9374726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21123.351191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2915569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3511535
X-RAY DIFFRACTIONr_chiral_restr0.0960.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212814
X-RAY DIFFRACTIONr_mcbond_it0.71.52051
X-RAY DIFFRACTIONr_mcangle_it1.28123349
X-RAY DIFFRACTIONr_scbond_it2.01231404
X-RAY DIFFRACTIONr_scangle_it3.3314.51377
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 156 -
Rwork0.342 3046 -
all-3202 -
obs--99.84 %
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)
11.3308-0.5076-0.17980.66360.19580.23110.04040.12140.0981-0.0617-0.0217-0.0336-0.03120.0147-0.01870.0865-0.00340.0060.07280.02010.05878.194-6.3357-33.3621
21.2822-0.0424-0.46610.68430.30110.3224-0.04620.0035-0.073800.01980.08040.0523-0.00430.02630.08320.0008-0.00360.05740.00290.0744-1.3627-14.5705-25.284
30.4072-0.2269-0.03580.59430.14330.2635-0.04480.0681-0.0959-0.05660.00320.07490.01420.04120.04160.0614-0.0003-0.00020.0497-0.00860.06189.0627-19.9985-27.6278
40.39350.0630.92490.1819-0.08323.02730.1109-0.0835-0.01750.05790.0716-0.05090.3197-0.3391-0.18260.14540.0074-0.050.1166-0.00610.093322.9741-16.32260.1565
50.3531-0.03780.7980.43510.03523.48060.0631-0.03070.07030.06110.0593-0.13950.34610.1301-0.12230.11520.0356-0.0510.0992-0.03370.099527.2131-15.6742-3.4854
611.38952.11811.00886.20480.29783.54960.07690.0598-0.1911-0.14860.02420.4860.1825-0.3505-0.10120.14890.01390.01920.11090.00570.07490.4369-5.6233-10.1081
72.090.69640.48320.72150.22680.6817-0.121-0.09160.23460.03680.0818-0.0325-0.09680.02040.03920.10190.0097-0.0480.0536-0.03130.10118.3564.4637-12.4822
82.60861.49880.46242.02020.40150.5943-0.0701-0.0035-0.0103-0.00410.0569-0.1905-0.0601-0.02990.01310.09130.0177-0.01030.05590.00230.0711.7698-3.7707-19.1805
96.94281.84550.17810.7175-0.32880.722-0.0131-0.30420.59960.1814-0.01840.1115-0.2663-0.04450.03150.17290.0687-0.05470.105-0.13130.179715.28867.7702-6.605
104.6925-1.30660.65223.5741-0.00213.0805-0.041-0.50850.33450.4763-0.0411-0.0796-0.03760.08020.08210.11910.0199-0.04740.1145-0.07610.065919.03933.0601-3.08
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 78
2X-RAY DIFFRACTION2A79 - 123
3X-RAY DIFFRACTION3A124 - 194
4X-RAY DIFFRACTION4A195 - 231
5X-RAY DIFFRACTION5A232 - 276
6X-RAY DIFFRACTION6B0 - 6
7X-RAY DIFFRACTION7B7 - 49
8X-RAY DIFFRACTION8B50 - 69
9X-RAY DIFFRACTION9B70 - 89
10X-RAY DIFFRACTION10B90 - 99

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