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- PDB-5e8o: The structure of the TEIPP associated altered peptide ligand Trh4... -

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Basic information

Entry
Database: PDB / ID: 5e8o
TitleThe structure of the TEIPP associated altered peptide ligand Trh4-p2ABU in complex with H-2D(b)
Components
  • Beta-2-microglobulinBeta-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-canonical peptide binding
Function / homology
Function and homology information


sphingosine N-acyltransferase / sphingoid base N-palmitoyltransferase / Sphingolipid de novo biosynthesis / sphingosine N-acyltransferase activity / sphingolipid biosynthetic process / ceramide biosynthetic process / TAP1 binding / TAP2 binding / negative regulation of natural killer cell activation / positive regulation of antibody-dependent cellular cytotoxicity ...sphingosine N-acyltransferase / sphingoid base N-palmitoyltransferase / Sphingolipid de novo biosynthesis / sphingosine N-acyltransferase activity / sphingolipid biosynthetic process / ceramide biosynthetic process / TAP1 binding / TAP2 binding / 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 activation / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / 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 / 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 / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / negative regulation of T cell proliferation / protection from natural killer cell mediated cytotoxicity / 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 / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / 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 / 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 / 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 / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / positive regulation of type II interferon production / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / iron ion transport / antibacterial humoral response / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization
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 / 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 / Ceramide synthase 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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

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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
C: Ceramide synthase 5
B: Beta-2-microglobulin
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)89,6616
Polymers89,6616
Non-polymers00
Water2,072115
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
C: Ceramide synthase 5
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)44,8303
Polymers44,8303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-23 kcal/mol
Surface area19520 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 area4280 Å2
ΔGint-24 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.859, 123.330, 97.552
Angle α, β, γ (deg.)90.00, 104.67, 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/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: 1038.372 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
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 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: Jan 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.98→32.329 Å / Num. obs: 71202 / % possible obs: 98.61 % / Observed criterion σ(I): 9 / Redundancy: 6.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9
Reflection shellResolution: 1.98→2.02 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 97.9

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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: 1.98→32.329 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 3588 5.04 %
Rwork0.218 --
obs0.2198 71202 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→32.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6209 0 0 115 6324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086414
X-RAY DIFFRACTIONf_angle_d0.968717
X-RAY DIFFRACTIONf_dihedral_angle_d15.3853815
X-RAY DIFFRACTIONf_chiral_restr0.056882
X-RAY DIFFRACTIONf_plane_restr0.0071139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00610.32521390.29622584X-RAY DIFFRACTION98
2.0061-2.03350.33681230.2862581X-RAY DIFFRACTION98
2.0335-2.06260.26861310.28362596X-RAY DIFFRACTION98
2.0626-2.09340.29661260.25962551X-RAY DIFFRACTION98
2.0934-2.12610.31981400.25822591X-RAY DIFFRACTION98
2.1261-2.16090.2821450.252599X-RAY DIFFRACTION98
2.1609-2.19820.29371470.24432519X-RAY DIFFRACTION98
2.1982-2.23810.27151330.25682598X-RAY DIFFRACTION98
2.2381-2.28120.34421330.24922603X-RAY DIFFRACTION98
2.2812-2.32770.29541490.24542586X-RAY DIFFRACTION98
2.3277-2.37830.3061340.25012580X-RAY DIFFRACTION99
2.3783-2.43360.26831450.24922576X-RAY DIFFRACTION99
2.4336-2.49450.26041430.23442615X-RAY DIFFRACTION98
2.4945-2.56190.28661410.2362588X-RAY DIFFRACTION99
2.5619-2.63720.27251360.24612590X-RAY DIFFRACTION99
2.6372-2.72230.30521300.24662600X-RAY DIFFRACTION98
2.7223-2.81960.3111230.25462616X-RAY DIFFRACTION99
2.8196-2.93240.27971470.26122613X-RAY DIFFRACTION99
2.9324-3.06570.30531440.25992575X-RAY DIFFRACTION99
3.0657-3.22720.28511340.2522654X-RAY DIFFRACTION99
3.2272-3.42920.27831410.22872576X-RAY DIFFRACTION99
3.4292-3.69360.23421430.20162635X-RAY DIFFRACTION99
3.6936-4.06470.20711250.17572653X-RAY DIFFRACTION99
4.0647-4.65140.18141490.15882625X-RAY DIFFRACTION99
4.6514-5.85460.18961460.16652632X-RAY DIFFRACTION99
5.8546-32.33310.22291410.18422678X-RAY DIFFRACTION99

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