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- PDB-5ts1: Crystal structure of MHC-I H2-KD complexed with peptides of Mycob... -

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Basic information

Entry
Database: PDB / ID: 5ts1
TitleCrystal structure of MHC-I H2-KD complexed with peptides of Mycobacterial tuberculosis (YYQSGLSIV)
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 class I histocompatibility antigen, K-D alpha chain
  • Peptide (P9) of Mtb85B (Mycobacterium tuberculosis) YYQSGLSIV
KeywordsIMMUNE SYSTEM / MAJOR HISTOMPATIBILITY COMPLEX CLASS I / MHC-I / H2-Kd / H-2Kd / Mycobacterial tuberculosis / TB peptide / Mtb85B / Mtb85A / Mkan85B / IMMUNE RESPONSE
Function / homology
Function and homology information


trehalose O-mycolyltransferase / trehalose O-mycolyltransferase activity / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / regulation of growth rate / positive regulation of plasminogen activation / response to host immune response / zymogen binding / TAP1 binding / TAP2 binding ...trehalose O-mycolyltransferase / trehalose O-mycolyltransferase activity / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / regulation of growth rate / positive regulation of plasminogen activation / response to host immune response / zymogen binding / TAP1 binding / TAP2 binding / 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 tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / acyltransferase activity, transferring groups other than amino-acyl groups / positive regulation of natural killer cell mediated cytotoxicity / inner ear development / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / fibronectin binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / peptidoglycan-based cell wall / 14-3-3 protein binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / 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 / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / positive regulation of type II interferon production / sensory perception of smell
Similarity search - Function
Esterase-like / Putative esterase / 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 ...Esterase-like / Putative esterase / 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. / Alpha/Beta hydrolase fold / 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
H-2 class I histocompatibility antigen, K-D alpha chain / Beta-2-microglobulin / Diacylglycerol acyltransferase/mycolyltransferase Ag85B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsJiang, J. / Natarajan, K. / Margulies, D.
CitationJournal: Eur.J.Immunol. / Year: 2019
Title: MHC-restricted Ag85B-specific CD8+T cells are enhanced by recombinant BCG prime and DNA boost immunization in mice.
Authors: Komine-Aizawa, S. / Jiang, J. / Mizuno, S. / Hayakawa, S. / Matsuo, K. / Boyd, L.F. / Margulies, D.H. / Honda, M.
History
DepositionOct 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / 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 2.0Feb 5, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / refine_hist
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-D alpha chain
B: Beta-2-microglobulin
P: Peptide (P9) of Mtb85B (Mycobacterium tuberculosis) YYQSGLSIV
C: H-2 class I histocompatibility antigen, K-D alpha chain
D: Beta-2-microglobulin
Q: Peptide (P9) of Mtb85B (Mycobacterium tuberculosis) YYQSGLSIV
E: H-2 class I histocompatibility antigen, K-D alpha chain
F: Beta-2-microglobulin
R: Peptide (P9) of Mtb85B (Mycobacterium tuberculosis) YYQSGLSIV
G: H-2 class I histocompatibility antigen, K-D alpha chain
H: Beta-2-microglobulin
S: Peptide (P9) of Mtb85B (Mycobacterium tuberculosis) YYQSGLSIV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,03221
Polymers180,29312
Non-polymers7399
Water8,503472
1
A: H-2 class I histocompatibility antigen, K-D alpha chain
B: Beta-2-microglobulin
P: Peptide (P9) of Mtb85B (Mycobacterium tuberculosis) YYQSGLSIV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3206
Polymers45,0733
Non-polymers2463
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-13 kcal/mol
Surface area18300 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, K-D alpha chain
D: Beta-2-microglobulin
Q: Peptide (P9) of Mtb85B (Mycobacterium tuberculosis) YYQSGLSIV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2906
Polymers45,0733
Non-polymers2163
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-11 kcal/mol
Surface area18810 Å2
MethodPISA
3
E: H-2 class I histocompatibility antigen, K-D alpha chain
F: Beta-2-microglobulin
R: Peptide (P9) of Mtb85B (Mycobacterium tuberculosis) YYQSGLSIV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1654
Polymers45,0733
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-17 kcal/mol
Surface area18390 Å2
MethodPISA
4
G: H-2 class I histocompatibility antigen, K-D alpha chain
H: Beta-2-microglobulin
S: Peptide (P9) of Mtb85B (Mycobacterium tuberculosis) YYQSGLSIV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2575
Polymers45,0733
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-17 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.302, 88.960, 109.947
Angle α, β, γ (deg.)89.97, 93.83, 90.04
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
H-2 class I histocompatibility antigen, K-D alpha chain / H-2K(D)


Mass: 32164.770 Da / Num. of mol.: 4 / Fragment: UNP residues 23-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Plasmid: PET21-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01902
#2: Protein
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 4 / Fragment: residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769

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Protein/peptide , 1 types, 4 molecules PQRS

#3: Protein/peptide
Peptide (P9) of Mtb85B (Mycobacterium tuberculosis) YYQSGLSIV / DGAT / 30 kDa extracellular protein / Acyl-CoA:diacylglycerol acyltransferase / Antigen 85 complex ...DGAT / 30 kDa extracellular protein / Acyl-CoA:diacylglycerol acyltransferase / Antigen 85 complex B / Ag85B / Extracellular alpha-antigen / Fibronectin-binding protein B / Fbps B


Mass: 1029.145 Da / Num. of mol.: 4 / Fragment: UNP residues 101-109 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: P9WQP1

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Non-polymers , 3 types, 481 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 14% PEG 4000, 0.1M MES buffer, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0333 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 24, 2016
RadiationMonochromator: SI 100 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 2.3→47.2 Å / Num. obs: 78047 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.232 / Net I/σ(I): 6.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.488 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.3→47.2 Å / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.59
RfactorNum. reflection% reflection
Rfree0.2239 3975 5.09 %
Rwork0.1868 --
obs0.1893 78047 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 21.6 Å2 / ksol: 0.34 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12626 0 48 472 13146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713049
X-RAY DIFFRACTIONf_angle_d1.20117720
X-RAY DIFFRACTIONf_dihedral_angle_d20.4197651
X-RAY DIFFRACTIONf_chiral_restr0.0711796
X-RAY DIFFRACTIONf_plane_restr0.0092298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33970.31991950.24493696X-RAY DIFFRACTION92
2.3397-2.38220.30151920.23673658X-RAY DIFFRACTION93
2.3822-2.42810.29581930.22123661X-RAY DIFFRACTION92
2.4281-2.47760.29391970.23413731X-RAY DIFFRACTION93
2.4776-2.53150.26861930.21383668X-RAY DIFFRACTION93
2.5315-2.59040.24111940.21373688X-RAY DIFFRACTION93
2.5904-2.65520.27011950.21123720X-RAY DIFFRACTION93
2.6552-2.72690.25611940.20223673X-RAY DIFFRACTION93
2.7269-2.80720.26321950.2023717X-RAY DIFFRACTION93
2.8072-2.89780.22831930.19283662X-RAY DIFFRACTION93
2.8978-3.00130.23271970.19673732X-RAY DIFFRACTION93
3.0013-3.12150.24381960.18513728X-RAY DIFFRACTION93
3.1215-3.26350.21811940.1843697X-RAY DIFFRACTION93
3.2635-3.43550.20221960.17763725X-RAY DIFFRACTION94
3.4355-3.65070.19481960.17443722X-RAY DIFFRACTION94
3.6507-3.93240.1981970.1683745X-RAY DIFFRACTION94
3.9324-4.32790.19081960.15083714X-RAY DIFFRACTION94
4.3279-4.95350.17841950.14443708X-RAY DIFFRACTION94
4.9535-6.23860.17811970.17023745X-RAY DIFFRACTION94
6.2386-46.7080.25311980.22853749X-RAY DIFFRACTION94

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