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- PDB-5e8p: The structure of the TEIPP associated altered peptide ligand Trh4... -

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Basic information

Entry
Database: PDB / ID: 5e8p
TitleThe structure of the TEIPP associated altered peptide ligand Trh4-p5NLE in complex with H-2D(b)
Components
  • Beta-2-microglobulin
  • Ceramide synthase 5
  • H-2 class I histocompatibility antigen, D-B alpha chain
KeywordsIMMUNE SYSTEM / Cancer / Neo-epitope / TAP-deficiency / TEIPP / MHC-I / Sulfur-pi interactions / Non-classical peptide binding
Function / homology
Function and homology information


sphingosine N-acyltransferase / Sphingolipid de novo biosynthesis / sphingoid base N-palmitoyltransferase / sphingosine N-acyltransferase activity / sphingolipid biosynthetic process / ceramide biosynthetic process / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway ...sphingosine N-acyltransferase / Sphingolipid de novo biosynthesis / sphingoid base N-palmitoyltransferase / sphingosine N-acyltransferase activity / sphingolipid biosynthetic process / ceramide biosynthetic process / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / MHC class I protein complex / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / external side of plasma membrane / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / DNA binding / plasma membrane / cytosol
Similarity search - Function
TRAM/LAG1/CLN8 homology domain / Sphingosine N-acyltransferase Lag1/Lac1-like / TLC domain / TLC domain profile. / TRAM, LAG1 and CLN8 homology domains. / Homeodomain / Homeobox domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like ...TRAM/LAG1/CLN8 homology domain / Sphingosine N-acyltransferase Lag1/Lac1-like / TLC domain / TLC domain profile. / TRAM, LAG1 and CLN8 homology domains. / Homeodomain / Homeobox domain / 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 / Homeobox-like domain 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Ceramide synthase 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHafstrand, I. / Doorduijn, E. / Duru, A.D. / Buratto, J. / Oliveira, C.C. / Sandalova, T. / van Hall, T. / Achour, A.
CitationJournal: J Immunol. / Year: 2016
Title: The MHC Class I Cancer-Associated Neoepitope Trh4 Linked with Impaired Peptide Processing Induces a Unique Noncanonical TCR Conformer.
Authors: Hafstrand, I. / Doorduijn, E.M. / Duru, A.D. / Buratto, J. / Oliveira, C.C. / Sandalova, T. / van Hall, T. / Achour, A.
History
DepositionOct 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Jan 10, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Ceramide synthase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7577
Polymers89,6616
Non-polymers961
Water4,414245
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Ceramide synthase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9264
Polymers44,8303
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-35 kcal/mol
Surface area18960 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Ceramide synthase 5


Theoretical massNumber of molelcules
Total (without water)44,8303
Polymers44,8303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-25 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.590, 123.772, 97.683
Angle α, β, γ (deg.)90.00, 104.31, 90.00
Int Tables number5
Space group name H-MI121

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Components

#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


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
#3: Protein/peptide Ceramide synthase 5 / CerS5 / LAG1 longevity assurance homolog 5 / Translocating chain-associating membrane protein ...CerS5 / LAG1 longevity assurance homolog 5 / Translocating chain-associating membrane protein homolog 4 / TRAM homolog 4


Mass: 1038.371 Da / Num. of mol.: 2 / Fragment: UNP residues 379-387 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9D6K9, sphingosine N-acyltransferase
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6 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: ESRF / Beamline: ID14-2 / Wavelength: 0.965 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2013 / Details: ID30A-1/MASSIF-1, PILATUS3 2M
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2→32.3 Å / Num. obs: 68583 / % possible obs: 96.5 % / Observed criterion σ(I): 4.2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.2
Reflection shellResolution: 2→2.04 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S7U

1s7u


Resolution: 2→31.802 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2575 3382 4.95 %
Rwork0.2145 --
obs0.2166 68358 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→31.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 5 245 6470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096455
X-RAY DIFFRACTIONf_angle_d1.198767
X-RAY DIFFRACTIONf_dihedral_angle_d17.4123849
X-RAY DIFFRACTIONf_chiral_restr0.056883
X-RAY DIFFRACTIONf_plane_restr0.0071143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.02860.311370.28042740X-RAY DIFFRACTION98
2.0286-2.05890.37571510.30432700X-RAY DIFFRACTION97
2.0589-2.09110.39061300.34662625X-RAY DIFFRACTION95
2.0911-2.12530.31161410.26092682X-RAY DIFFRACTION97
2.1253-2.1620.31311360.24632679X-RAY DIFFRACTION96
2.162-2.20130.30941110.24322685X-RAY DIFFRACTION96
2.2013-2.24360.36381320.312594X-RAY DIFFRACTION94
2.2436-2.28940.31021510.29252667X-RAY DIFFRACTION96
2.2894-2.33920.26761320.22762715X-RAY DIFFRACTION99
2.3392-2.39360.27981300.22132745X-RAY DIFFRACTION98
2.3936-2.45340.26721390.22682756X-RAY DIFFRACTION99
2.4534-2.51970.25081550.21652738X-RAY DIFFRACTION99
2.5197-2.59380.26241480.23472732X-RAY DIFFRACTION99
2.5938-2.67750.3021490.2372724X-RAY DIFFRACTION98
2.6775-2.77310.34651410.2392732X-RAY DIFFRACTION98
2.7731-2.88410.27951400.23152703X-RAY DIFFRACTION97
2.8841-3.01530.2951540.23212702X-RAY DIFFRACTION97
3.0153-3.17410.29831660.2332661X-RAY DIFFRACTION97
3.1741-3.37280.25891540.21712683X-RAY DIFFRACTION97
3.3728-3.63280.22951420.19342746X-RAY DIFFRACTION98
3.6328-3.99780.19551370.17382725X-RAY DIFFRACTION97
3.9978-4.57480.18191340.14992710X-RAY DIFFRACTION97
4.5748-5.75820.16711260.162754X-RAY DIFFRACTION97
5.7582-31.80620.21431460.18322778X-RAY DIFFRACTION98

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