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- PDB-6zkx: Crystal structure of InhA:01 TCR in complex with HLA-E (Y84C) bou... -

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Basic information

Entry
Database: PDB / ID: 6zkx
TitleCrystal structure of InhA:01 TCR in complex with HLA-E (Y84C) bound to InhA (53-61 GCG)
Components
  • (T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • Enoyl-[acyl-carrier-protein] reductase [NADH]
  • HLA class I histocompatibility antigen, alpha chain E
KeywordsIMMUNE SYSTEM / T cell receptor / TCR / HLA-E / InhA
Function / homology
Function and homology information


positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / fatty acid elongation / negative regulation of natural killer cell mediated cytotoxicity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 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 / positive regulation of immunoglobulin production / positive regulation of interleukin-4 production / beta-2-microglobulin binding / positive regulation of natural killer cell proliferation / MHC class I protein 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 / NAD+ binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / T cell receptor binding / negative regulation of T cell proliferation / peptidoglycan-based cell wall / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / fatty acid binding / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / positive regulation of tumor necrosis factor production / 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 / antibacterial humoral response / 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 / adaptive immune response / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / receptor ligand activity / endoplasmic reticulum lumen / Amyloid fiber formation
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / 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 / Short-chain dehydrogenase/reductase SDR / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / 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 / Short-chain dehydrogenase/reductase SDR / 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 / NAD(P)-binding 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, alpha chain E / Beta-2-microglobulin / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsSrikannathasan, V. / Karuppiah, V. / Robinson, R.A.
CitationJournal: Eur.J.Immunol. / Year: 2022
Title: Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition.
Authors: Barber, C. / De Souza, V.A. / Paterson, R.L. / Martin-Urdiroz, M. / Mulakkal, N.C. / Srikannathasan, V. / Connolly, M. / Phillips, G. / Foong-Leong, T. / Pengelly, R. / Karuppiah, V. / ...Authors: Barber, C. / De Souza, V.A. / Paterson, R.L. / Martin-Urdiroz, M. / Mulakkal, N.C. / Srikannathasan, V. / Connolly, M. / Phillips, G. / Foong-Leong, T. / Pengelly, R. / Karuppiah, V. / Grant, T. / Dembek, M. / Verma, A. / Gibbs-Howe, D. / Blicher, T.H. / Knox, A. / Robinson, R.A. / Cole, D.K. / Leonard, S.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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, alpha chain E
B: Beta-2-microglobulin
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: T-cell receptor alpha chain
E: T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,45713
Polymers93,9605
Non-polymers4978
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13350 Å2
ΔGint-28 kcal/mol
Surface area36780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.870, 107.860, 119.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, alpha chain E / MHC class I antigen E


Mass: 31895.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Production host: Escherichia coli (E. coli) / References: UniProt: P13747
#2: Protein Beta-2-microglobulin


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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


Mass: 1197.494 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)

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T-cell receptor ... , 2 types, 2 molecules DE

#4: Protein T-cell receptor alpha chain


Mass: 21496.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein T-cell receptor beta chain


Mass: 27491.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 265 molecules

#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 25% (w/v) PEG 4000, 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.17→79.93 Å / Num. obs: 49326 / % possible obs: 99.31 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.04 / Net I/σ(I): 12.8
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.342 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2415 / CC1/2: 0.581 / Rpim(I) all: 0.579 / % possible all: 98.89

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W1W, 5EU6

5w1w

5eu6


Resolution: 2.17→79.93 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.675 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24419 2369 4.8 %RANDOM
Rwork0.20908 ---
obs0.21081 46900 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.68 Å2
Baniso -1Baniso -2Baniso -3
1-4.5 Å20 Å20 Å2
2---1.48 Å20 Å2
3----3.02 Å2
Refinement stepCycle: 1 / Resolution: 2.17→79.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6522 0 32 257 6811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136755
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175912
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.6519175
X-RAY DIFFRACTIONr_angle_other_deg1.081.57513769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.435.266846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56622.461382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.684151067
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8061545
X-RAY DIFFRACTIONr_chiral_restr0.0360.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021461
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3234.9163297
X-RAY DIFFRACTIONr_mcbond_other1.3234.9143296
X-RAY DIFFRACTIONr_mcangle_it2.3127.3654117
X-RAY DIFFRACTIONr_mcangle_other2.3117.3674118
X-RAY DIFFRACTIONr_scbond_it1.2055.0073458
X-RAY DIFFRACTIONr_scbond_other1.2055.0073459
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.047.4475057
X-RAY DIFFRACTIONr_long_range_B_refined3.84754.0496936
X-RAY DIFFRACTIONr_long_range_B_other3.82153.9856910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 163 -
Rwork0.318 3406 -
obs--98.95 %

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