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- PDB-5mzm: Structure of H-2Db in complex with TEIPP APL Trh4 p3P -

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Basic information

Entry
Database: PDB / ID: 5mzm
TitleStructure of H-2Db in complex with TEIPP APL Trh4 p3P
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Ceramide synthase 5 derived peptide Trh4 p3P
  • H-2 class I histocompatibility antigen, D-B alpha chain
KeywordsIMMUNE SYSTEM / cancer / neo-epitope / T-cell epitopes associated with impaired peptide processing / MHC-I
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / beta-2-microglobulin binding ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / beta-2-microglobulin binding / Neutrophil degranulation / 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 / lumenal side of endoplasmic reticulum membrane / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / 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 / positive regulation of immune response / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / iron ion transport / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / 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 classes I/II-like antigen recognition protein ...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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHafstrand, I. / Achour, A. / Sandalova, T.
CitationJournal: J. Immunol. / Year: 2018
Title: The Immunogenicity of a Proline-Substituted Altered Peptide Ligand toward the Cancer-Associated TEIPP Neoepitope Trh4 Is Unrelated to Complex Stability.
Authors: Hafstrand, I. / Doorduijn, E.M. / Sun, R. / Talyzina, A. / Sluijter, M. / Pellegrino, S. / Sandalova, T. / Duru, A.D. / van Hall, T. / Achour, A.
History
DepositionFeb 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Ceramide synthase 5 derived peptide Trh4 p3P
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Ceramide synthase 5 derived peptide Trh4 p3P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9499
Polymers89,6656
Non-polymers2843
Water2,360131
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Ceramide synthase 5 derived peptide Trh4 p3P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1176
Polymers44,8323
Non-polymers2843
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-43 kcal/mol
Surface area19840 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Ceramide synthase 5 derived peptide Trh4 p3P


Theoretical massNumber of molelcules
Total (without water)44,8323
Polymers44,8323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-24 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.350, 125.010, 98.053
Angle α, β, γ (deg.)90.00, 103.53, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein , 2 types, 4 molecules ADBE

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


Mass: 32087.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Ceramide synthase 5 derived peptide Trh4 p3P


Mass: 1040.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: synthetic construct (others)

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Non-polymers , 3 types, 134 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2 M Ammonium sulphate, 0.1 M Tris-HCl, 0.5 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.4→58.5 Å / Num. obs: 41766 / % possible obs: 99.9 % / Redundancy: 3.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.087 / Net I/σ(I): 7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4378 / CC1/2: 0.913 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S7U

1s7u


Resolution: 2.4→36.201 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.97
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 2280 5.46 %random
Rwork0.2263 ---
obs0.2286 41747 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→36.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6234 0 16 131 6381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036454
X-RAY DIFFRACTIONf_angle_d0.6578758
X-RAY DIFFRACTIONf_dihedral_angle_d12.6533853
X-RAY DIFFRACTIONf_chiral_restr0.043876
X-RAY DIFFRACTIONf_plane_restr0.0051140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45220.34981520.30452433X-RAY DIFFRACTION100
2.4522-2.50920.32461470.25712454X-RAY DIFFRACTION100
2.5092-2.5720.30441660.26752414X-RAY DIFFRACTION100
2.572-2.64150.32321170.25922488X-RAY DIFFRACTION100
2.6415-2.71920.32591230.2652474X-RAY DIFFRACTION100
2.7192-2.80690.32681360.26852483X-RAY DIFFRACTION100
2.8069-2.90720.28951370.26222467X-RAY DIFFRACTION100
2.9072-3.02350.28921610.26362448X-RAY DIFFRACTION100
3.0235-3.16110.32561410.2512493X-RAY DIFFRACTION100
3.1611-3.32760.29461320.23632442X-RAY DIFFRACTION100
3.3276-3.53590.26831580.232460X-RAY DIFFRACTION100
3.5359-3.80870.2711220.21162493X-RAY DIFFRACTION100
3.8087-4.19150.26981520.20572450X-RAY DIFFRACTION100
4.1915-4.79680.23441520.19642480X-RAY DIFFRACTION100
4.7968-6.03890.22911550.19862466X-RAY DIFFRACTION100
6.0389-36.20470.19221290.20262522X-RAY DIFFRACTION99
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)
14.10370.25950.18032.0774-0.48352.69920.11490.10550.5569-0.08260.0396-0.4218-0.32760.5481-0.10650.3181-0.06510.06750.2862-0.03760.23971.57896.815886.2147
23.3676-0.2402-1.37522.65680.80321.8939-0.14110.3021-0.2891-0.10760.0273-0.04340.1305-0.02420.10470.2863-0.01430.02250.2304-0.0020.2139-7.8117-4.993486.0532
33.342-0.39790.53194.62140.36142.0360.1076-0.3605-0.77180.98130.2251-0.11560.29140.1899-0.31080.55810.0209-0.12260.3639-0.07480.60219.809-10.029119.6551
41.69461.05641.26111.53590.95123.1322-0.0629-0.17750.1976-0.05060.1581-0.1803-0.37970.301-0.07980.2759-0.0590.03090.3697-0.09370.25594.955110.8377111.6894
51.0177-0.06351.12090.0928-0.14781.46890.18890.83860.2018-0.1011-0.0982-0.27760.096-0.0839-0.06340.4717-0.00220.07540.42530.05450.3207-6.25711.183879.7138
62.10980.63140.99754.18370.24862.96140.0646-0.3073-0.57720.15980.2201-1.11030.18450.3764-0.27610.22150.0829-0.07720.3124-0.07280.4312-1.6199-45.671106.7044
72.2077-0.09350.25482.11040.87651.0427-0.1073-0.12690.41340.16380.08660.0645-0.19920.0164-0.01660.27160.0233-0.07830.197-0.01830.2394-12.0298-31.8924106.5237
82.25570.7237-0.07313.7142-0.23991.58780.12280.44760.4508-0.89650.1001-0.5697-0.17760.0457-0.07180.39330.0660.12760.397-0.0380.653211.4718-29.873879.6589
93.0358-1.4888-2.17991.85721.18393.1031-0.18110.1924-0.1245-0.05280.1827-0.11710.3310.01510.03590.2688-0.02240.02090.288-0.07550.28946.3742-50.48182.8227
104.05640.9957-2.37981.648-0.73721.3412-0.1588-0.92410.4250.51270.2742-0.292-0.36970.1413-0.22940.53750.0304-0.12930.4096-0.06790.3006-8.2119-40.216112.9341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 174 )
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 276 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 99 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 9 )
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 103 )
7X-RAY DIFFRACTION7chain 'D' and (resid 104 through 162 )
8X-RAY DIFFRACTION8chain 'D' and (resid 163 through 276 )
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 99)
10X-RAY DIFFRACTION10chain 'F' and (resid 1 through 9 )

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