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- PDB-5e8n: The structure of the TEIPP associated Trh4 peptide in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5e8n
TitleThe structure of the TEIPP associated Trh4 peptide 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: 2.25 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 1.4Nov 20, 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
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: Ceramide synthase 5
J: H-2 class I histocompatibility antigen, D-B alpha chain
K: Beta-2-microglobulin
L: Ceramide synthase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,58214
Polymers179,39412
Non-polymers1882
Water2,432135
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)44,9414
Polymers44,8483
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-23 kcal/mol
Surface area19450 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)44,8483
Polymers44,8483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-25 kcal/mol
Surface area19610 Å2
MethodPISA
3
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: Ceramide synthase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9454
Polymers44,8483
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-31 kcal/mol
Surface area19030 Å2
MethodPISA
4
J: H-2 class I histocompatibility antigen, D-B alpha chain
K: Beta-2-microglobulin
L: Ceramide synthase 5


Theoretical massNumber of molelcules
Total (without water)44,8483
Polymers44,8483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-23 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.510, 124.250, 99.290
Angle α, β, γ (deg.)90.00, 103.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ADGJBEHK

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


Mass: 32087.703 Da / Num. of mol.: 4
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.: 4
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, 4 molecules CFIL

#3: Protein/peptide
Ceramide synthase 5 / Trh4 / CerS5 / LAG1 longevity assurance homolog 5 / Translocating chain-associating membrane ...Trh4 / CerS5 / LAG1 longevity assurance homolog 5 / Translocating chain-associating membrane protein homolog 4 / TRAM homolog 4


Mass: 1056.410 Da / Num. of mol.: 4 / Fragment: UNP residues 379-387 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9D6K9, sphingosine N-acyltransferase

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Non-polymers , 3 types, 137 molecules

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


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


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


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.9 M Ammonium sulphate, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.24→52.26 Å / Num. obs: 102342 / % possible obs: 98.85 % / Observed criterion σ(I): 6.1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.5
Reflection shellResolution: 2.24→2.25 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 5028 / % possible all: 99.7

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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: 2.25→52.259 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2863 5028 4.92 %
Rwork0.2392 --
obs0.2416 102292 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→52.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12301 0 11 135 12447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912747
X-RAY DIFFRACTIONf_angle_d1.06117314
X-RAY DIFFRACTIONf_dihedral_angle_d17.0977588
X-RAY DIFFRACTIONf_chiral_restr0.0571743
X-RAY DIFFRACTIONf_plane_restr0.0072258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.27560.39731720.3273215X-RAY DIFFRACTION100
2.2756-2.30230.36981470.32423301X-RAY DIFFRACTION100
2.3023-2.33040.36511500.3183219X-RAY DIFFRACTION100
2.3304-2.35990.39261740.32743280X-RAY DIFFRACTION100
2.3599-2.3910.41091960.32023273X-RAY DIFFRACTION100
2.391-2.42370.37131770.30623234X-RAY DIFFRACTION100
2.4237-2.45840.35551700.28523235X-RAY DIFFRACTION100
2.4584-2.4950.30791700.28123267X-RAY DIFFRACTION100
2.495-2.5340.32521590.28083255X-RAY DIFFRACTION100
2.534-2.57560.3371600.27533285X-RAY DIFFRACTION100
2.5756-2.620.32171740.28313216X-RAY DIFFRACTION100
2.62-2.66760.3241740.27853252X-RAY DIFFRACTION100
2.6676-2.71890.34531630.27883291X-RAY DIFFRACTION100
2.7189-2.77440.33471530.28983246X-RAY DIFFRACTION100
2.7744-2.83480.35871600.28243279X-RAY DIFFRACTION100
2.8348-2.90070.30221610.27073257X-RAY DIFFRACTION99
2.9007-2.97320.34591710.27393255X-RAY DIFFRACTION99
2.9732-3.05360.35671630.27213260X-RAY DIFFRACTION99
3.0536-3.14340.30821510.26033236X-RAY DIFFRACTION99
3.1434-3.24490.2831780.26643248X-RAY DIFFRACTION99
3.2449-3.36090.28281740.25753256X-RAY DIFFRACTION99
3.3609-3.49540.30671590.2393265X-RAY DIFFRACTION99
3.4954-3.65440.29141900.21793217X-RAY DIFFRACTION99
3.6544-3.8470.25831670.20733261X-RAY DIFFRACTION99
3.847-4.0880.25991650.20913244X-RAY DIFFRACTION99
4.088-4.40350.21861520.19613272X-RAY DIFFRACTION98
4.4035-4.84630.23021890.1873197X-RAY DIFFRACTION98
4.8463-5.54690.25151690.19183240X-RAY DIFFRACTION98
5.5469-6.98590.27151850.2183199X-RAY DIFFRACTION97
6.9859-52.27290.20941550.20783009X-RAY DIFFRACTION89

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