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- PDB-6ujq: HHAT Wild Type Peptide KQWLVWLLL Presented by HLA-A206 -

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Basic information

Entry
Database: PDB / ID: 6ujq
TitleHHAT Wild Type Peptide KQWLVWLLL Presented by HLA-A206
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Protein-cysteine N-palmitoyltransferase HHAT
KeywordsIMMUNE SYSTEM / Neoantigen / Peptide/MHC
Function / homology
Function and homology information


N-terminal peptidyl-L-cysteine N-palmitoylation / O-acyltransferase activity / HHAT G278V doesn't palmitoylate Hh-Np / palmitoyltransferase activity / smoothened signaling pathway / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...N-terminal peptidyl-L-cysteine N-palmitoylation / O-acyltransferase activity / HHAT G278V doesn't palmitoylate Hh-Np / palmitoyltransferase activity / smoothened signaling pathway / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / Hedgehog ligand biogenesis / ER to Golgi transport vesicle membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / 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 / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family / 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 ...: / Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin / Protein-cysteine N-palmitoyltransferase HHAT / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsDevlin, J.R. / Baker, B.M. / Singh, N.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural dissimilarity from self drives neoepitope escape from immune tolerance.
Authors: Devlin, J.R. / Alonso, J.A. / Ayres, C.M. / Keller, G.L.J. / Bobisse, S. / Vander Kooi, C.W. / Coukos, G. / Gfeller, D. / Harari, A. / Baker, B.M.
History
DepositionOct 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.3Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: 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 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Protein-cysteine N-palmitoyltransferase HHAT


Theoretical massNumber of molelcules
Total (without water)45,0803
Polymers45,0803
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-24 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.027, 38.282, 116.350
Angle α, β, γ (deg.)90.000, 92.273, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein MHC class I antigen


Mass: 32001.398 Da / Num. of mol.: 1 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue / References: UniProt: U5YJP1
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue / References: UniProt: P61769
#3: Protein/peptide Protein-cysteine N-palmitoyltransferase HHAT


Mass: 1199.505 Da / Num. of mol.: 1 / Fragment: wild type peptide (UNP residues 68-76) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5VTY9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 0.1 M Tris-HCl, pH 8.1, 30% PEG4000, 0.20 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 13532 / % possible obs: 95.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 36.88 Å2 / CC1/2: 0.966 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.088 / Rrim(I) all: 0.161 / Net I/σ(I): 8
Reflection shellResolution: 2.55→2.61 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 813 / CC1/2: 0.671 / Rpim(I) all: 0.336 / Rrim(I) all: 0.589 / % possible all: 86.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.11.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TVH

1tvh


Resolution: 2.55→44.12 Å / SU ML: 0.3102 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4012
RfactorNum. reflection% reflection
Rfree0.2279 1354 10.01 %
Rwork0.1943 --
obs0.1977 13526 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.67 Å2
Refinement stepCycle: LAST / Resolution: 2.55→44.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 0 76 3247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663265
X-RAY DIFFRACTIONf_angle_d0.74364433
X-RAY DIFFRACTIONf_chiral_restr0.0543450
X-RAY DIFFRACTIONf_plane_restr0.0057575
X-RAY DIFFRACTIONf_dihedral_angle_d20.82641199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.640.33251140.2821026X-RAY DIFFRACTION81.43
2.64-2.750.311360.25651213X-RAY DIFFRACTION92.84
2.75-2.870.26651370.23741207X-RAY DIFFRACTION97.11
2.87-3.020.28441310.23511243X-RAY DIFFRACTION97.65
3.02-3.210.27071420.21421255X-RAY DIFFRACTION98.1
3.21-3.460.23031370.20471219X-RAY DIFFRACTION93.91
3.46-3.810.20881290.18321182X-RAY DIFFRACTION92.85
3.81-4.360.18461420.15391277X-RAY DIFFRACTION99.16
4.36-5.490.19731390.15591280X-RAY DIFFRACTION98.2
5.49-44.120.20851470.19671270X-RAY DIFFRACTION93.9
Refinement TLS params.Method: refined / Origin x: 21.1317450983 Å / Origin y: -30.4217162438 Å / Origin z: 29.5444007593 Å
111213212223313233
T0.242277942698 Å20.00514163378078 Å20.00292700234494 Å2-0.185427163746 Å2-0.00589461848981 Å2--0.237785472783 Å2
L0.429677637729 °2-0.0394642954137 °2-0.0373964928385 °2-0.646609015049 °2-0.00363622423617 °2--1.3347180861 °2
S0.00938988036917 Å °0.0298394178818 Å °0.0120255450763 Å °-0.0775100680087 Å °-0.0254584614855 Å °0.00257023429021 Å °-0.0170828043182 Å °-0.0381050657584 Å °0.0145999811592 Å °
Refinement TLS groupSelection details: all

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