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- PDB-6xqa: Crystal Structure of HLA A*2402 in complex with TYQWVLKNL, an 9-m... -

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Basic information

Entry
Database: PDB / ID: 6xqa
TitleCrystal Structure of HLA A*2402 in complex with TYQWVLKNL, an 9-mer epitope from Influenza B virus
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
  • PB2-549-557 peptide from Influenza B, TYQWVLKNL
KeywordsIMMUNE SYSTEM / HLA-A*2402 / influenza virus B / IBV / TCR / T cell
Function / homology
Function and homology information


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 / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent ...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 / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / 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 / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / 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. / Immunoglobulin C-Type / Immunoglobulin C1-set ...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 B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 Å
AuthorsNguyen, A.T. / Szeto, C. / Gras, S.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1122524 Australia
National Health and Medical Research Council (NHMRC, Australia)1159272 Australia
CitationJournal: Nat Commun / Year: 2021
Title: CD8 + T cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph.
Authors: Hensen, L. / Illing, P.T. / Bridie Clemens, E. / Nguyen, T.H.O. / Koutsakos, M. / van de Sandt, C.E. / Mifsud, N.A. / Nguyen, A.T. / Szeto, C. / Chua, B.Y. / Halim, H. / Rizzetto, S. / ...Authors: Hensen, L. / Illing, P.T. / Bridie Clemens, E. / Nguyen, T.H.O. / Koutsakos, M. / van de Sandt, C.E. / Mifsud, N.A. / Nguyen, A.T. / Szeto, C. / Chua, B.Y. / Halim, H. / Rizzetto, S. / Luciani, F. / Loh, L. / Grant, E.J. / Saunders, P.M. / Brooks, A.G. / Rockman, S. / Kotsimbos, T.C. / Cheng, A.C. / Richards, M. / Westall, G.P. / Wakim, L.M. / Loudovaris, T. / Mannering, S.I. / Elliott, M. / Tangye, S.G. / Jackson, D.C. / Flanagan, K.L. / Rossjohn, J. / Gras, S. / Davies, J. / Miller, A. / Tong, S.Y.C. / Purcell, A.W. / Kedzierska, K.
History
DepositionJul 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: 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
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: PB2-549-557 peptide from Influenza B, TYQWVLKNL
D: MHC class I antigen
E: Beta-2-microglobulin
F: PB2-549-557 peptide from Influenza B, TYQWVLKNL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0438
Polymers89,9946
Non-polymers492
Water10,575587
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: PB2-549-557 peptide from Influenza B, TYQWVLKNL


Theoretical massNumber of molelcules
Total (without water)44,9973
Polymers44,9973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-19 kcal/mol
Surface area18920 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: PB2-549-557 peptide from Influenza B, TYQWVLKNL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0465
Polymers44,9973
Non-polymers492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-31 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.066, 122.966, 86.590
Angle α, β, γ (deg.)90.000, 103.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MHC class I antigen / HLA-A*2402 heavy chain


Mass: 31952.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A411J078
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide PB2-549-557 peptide from Influenza B, TYQWVLKNL


Mass: 1165.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: influenza virus / Source: (synth.) Influenza B virus
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.6 % / Mosaicity: 0.15 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 24% PEG8000, 0.1 HEPES pH 7.5, 2% isopropanol, 5% w/v Polyvinylpyrrolidone K15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.16→44.81 Å / Num. obs: 49524 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 37.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.4 / Num. measured all: 188348 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.16-2.233.80.5381574441880.8192.696.9
8.92-44.813.50.01925567240.99949.797.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.1.27data scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F7M

4f7m


Resolution: 2.16→44.81 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.185
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2507 5.07 %RANDOM
Rwork0.179 ---
obs0.181 49496 98.5 %-
Displacement parametersBiso max: 126.55 Å2 / Biso mean: 35.14 Å2 / Biso min: 3.51 Å2
Baniso -1Baniso -2Baniso -3
1--7.4082 Å20 Å26.219 Å2
2--6.4114 Å20 Å2
3---0.9969 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 2.16→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6298 0 2 587 6887
Biso mean--39.06 40.54 -
Num. residues----768
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2243SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes180HARMONIC2
X-RAY DIFFRACTIONt_gen_planes939HARMONIC5
X-RAY DIFFRACTIONt_it6488HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion799SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7413SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6488HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8801HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion18.34
LS refinement shellResolution: 2.16→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2863 151 4.59 %
Rwork0.2048 3140 -
all0.2081 3291 -
obs--88.45 %

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