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- PDB-6j29: The structure of HLA-A*3003/MTB -

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Basic information

Entry
Database: PDB / ID: 6j29
TitleThe structure of HLA-A*3003/MTB
Components
  • Beta-2-microglobulin
  • HLA-A*3003
  • MTB
KeywordsIMMUNE SYSTEM / The structure of HLA-A*3003/MTB
Function / homology
Function and homology information


Inhibition of membrane repair / phagocytic vesicle lumen / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding ...Inhibition of membrane repair / phagocytic vesicle lumen / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / T cell receptor binding / Prevention of phagosomal-lysosomal fusion / : / : / 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 / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity
Similarity search - Function
ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / 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 ...ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / 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, A alpha chain / Beta-2-microglobulin / ESAT-6-like protein EsxH
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsZhu, S.Y. / Liu, K.F. / Chai, Y. / Ding, C.M. / Lv, J.X. / Gao, F.G. / Lou, Y.L. / Liu, W.J.
CitationJournal: Front Immunol / Year: 2019
Title: Divergent Peptide Presentations of HLA-A*30 Alleles Revealed by Structures With Pathogen Peptides.
Authors: Zhu, S. / Liu, K. / Chai, Y. / Wu, Y. / Lu, D. / Xiao, W. / Cheng, H. / Zhao, Y. / Ding, C. / Lyu, J. / Lou, Y. / Gao, G.F. / Liu, W.J.
History
DepositionDec 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: HLA-A*3003
C: MTB
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)44,4713
Polymers44,4713
Non-polymers00
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-20 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.825, 79.492, 44.823
Angle α, β, γ (deg.)90.00, 94.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-497-

HOH

21A-539-

HOH

31A-591-

HOH

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Components

#1: Protein HLA-A*3003


Mass: 31592.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P04439*PLUS
#2: Protein/peptide MTB


Mass: 1130.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: P9WNK3*PLUS
#3: Protein Beta-2-microglobulin / hB2m / FcRn light chain


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P61769
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Potassium Sodium Tartrate tetrahydrate, 0.1M Tri-Sodium Citrate dihydrate(pH 5.6), 2.0M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: SDMS / Detector: DIFFRACTOMETER / Date: Feb 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 72173 / % possible obs: 99.7 % / Redundancy: 6.8 % / Net I/σ(I): 0.8
Reflection shellResolution: 1.6→1.66 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 1.6→44.712 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 18.67
RfactorNum. reflection% reflection
Rfree0.1966 3505 4.86 %
Rwork0.1794 --
obs0.1802 72152 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→44.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 0 445 3578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133257
X-RAY DIFFRACTIONf_angle_d1.2414428
X-RAY DIFFRACTIONf_dihedral_angle_d28.7271216
X-RAY DIFFRACTIONf_chiral_restr0.089449
X-RAY DIFFRACTIONf_plane_restr0.008587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5927-1.61450.23611050.20782276X-RAY DIFFRACTION83
1.6145-1.63760.21711570.20122748X-RAY DIFFRACTION100
1.6376-1.6620.21181330.19662807X-RAY DIFFRACTION100
1.662-1.6880.26311310.19762708X-RAY DIFFRACTION100
1.688-1.71570.19161460.18652784X-RAY DIFFRACTION100
1.7157-1.74520.20741570.1852716X-RAY DIFFRACTION100
1.7452-1.7770.18581510.18362774X-RAY DIFFRACTION100
1.777-1.81120.22191360.18672742X-RAY DIFFRACTION99
1.8112-1.84810.2091360.18792748X-RAY DIFFRACTION100
1.8481-1.88830.17141120.19012792X-RAY DIFFRACTION100
1.8883-1.93220.20521390.18512768X-RAY DIFFRACTION100
1.9322-1.98060.21481350.17912782X-RAY DIFFRACTION100
1.9806-2.03410.22591390.18162801X-RAY DIFFRACTION100
2.0341-2.0940.21741380.18012723X-RAY DIFFRACTION100
2.094-2.16160.19951490.18032741X-RAY DIFFRACTION99
2.1616-2.23880.18381520.18552770X-RAY DIFFRACTION100
2.2388-2.32840.21171550.19022746X-RAY DIFFRACTION100
2.3284-2.43440.21681600.18732748X-RAY DIFFRACTION100
2.4344-2.56270.19771530.18942752X-RAY DIFFRACTION100
2.5627-2.72330.18531490.18822763X-RAY DIFFRACTION100
2.7233-2.93350.20231530.19742749X-RAY DIFFRACTION99
2.9335-3.22870.20241220.17952817X-RAY DIFFRACTION100
3.2287-3.69570.18971270.1642795X-RAY DIFFRACTION100
3.6957-4.65540.15381280.14272761X-RAY DIFFRACTION98
4.6554-44.72910.17821420.17572836X-RAY DIFFRACTION99

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