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- PDB-6ujo: HHAT L75F Neoantigen Peptide KQWLVWLFL Presented by HLA-A206 -

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Basic information

Entry
Database: PDB / ID: 6ujo
TitleHHAT L75F Neoantigen Peptide KQWLVWLFL 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 / positive regulation of receptor binding ...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 / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / Hedgehog ligand biogenesis / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / 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 / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / positive regulation of protein binding / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / 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 / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / iron ion transport / 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 / external side of plasma membrane / Golgi membrane / lysosomal 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: 2.25 Å
AuthorsDevlin, J.R. / Baker, B.M. / Vander Kooi, C.
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 1.5Nov 6, 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: MHC class I antigen
B: Beta-2-microglobulin
C: Protein-cysteine N-palmitoyltransferase HHAT


Theoretical massNumber of molelcules
Total (without water)45,1143
Polymers45,1143
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-21 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.541, 37.692, 120.113
Angle α, β, γ (deg.)90.000, 91.478, 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: 1233.521 Da / Num. of mol.: 1 / Fragment: Neoantigen peptide (UNP residues 68-76) / Mutation: L75F / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5VTY9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG3350, 0.1 M magnesium chloride, 0.1 M sodium citrate, pH 6.5

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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: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→28 Å / Num. obs: 19072 / % possible obs: 90.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.41 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.068 / Rrim(I) all: 0.129 / Net I/σ(I): 10.3
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1511 / CC1/2: 0.72 / Rpim(I) all: 0.289 / Rrim(I) all: 0.533 / % possible all: 87.2

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Processing

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

1tvh


Resolution: 2.25→26.54 Å / SU ML: 0.2511 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8285 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2218 1911 10.02 %
Rwork0.1719 17155 -
obs0.1769 19066 89.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.13 Å2
Refinement stepCycle: LAST / Resolution: 2.25→26.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 0 137 3311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00383269
X-RAY DIFFRACTIONf_angle_d0.64494438
X-RAY DIFFRACTIONf_chiral_restr0.0446449
X-RAY DIFFRACTIONf_plane_restr0.0037576
X-RAY DIFFRACTIONf_dihedral_angle_d18.18911199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.28051300.21691137X-RAY DIFFRACTION86.13
2.31-2.370.26151380.2291197X-RAY DIFFRACTION86.97
2.37-2.440.251280.21971239X-RAY DIFFRACTION94.47
2.44-2.520.25951430.22121279X-RAY DIFFRACTION92.7
2.52-2.610.27981430.21441292X-RAY DIFFRACTION96.5
2.61-2.710.27471440.21671252X-RAY DIFFRACTION92.39
2.71-2.830.30311400.20841214X-RAY DIFFRACTION91.67
2.83-2.980.26351360.1981198X-RAY DIFFRACTION88.58
2.98-3.170.25251130.18931042X-RAY DIFFRACTION75.79
3.17-3.410.2171430.17331311X-RAY DIFFRACTION95.09
3.41-3.760.16231470.15121293X-RAY DIFFRACTION94.55
3.76-4.30.16671430.13031288X-RAY DIFFRACTION95.34
4.3-5.410.19491350.12471247X-RAY DIFFRACTION89.22
5.41-26.540.21141280.15931166X-RAY DIFFRACTION80.93
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)
12.32447309215-0.659307206628-1.080695236382.256482460090.7479087119513.077366973450.0235070025763-0.0272362749097-0.0914022161529-0.00562876884557-0.04789540826060.03087686169730.01835388458420.01810882938020.0068860509620.1466791333790.0254744446457-0.04460749534510.1169172259790.03255997359420.14598136946327.4056558537-33.585524285744.3181933071
22.309092068730.5827211889230.1119658437613.15718200664-1.434219051153.534320858210.0489903328330.311545358530.1229013934780.0490751339843-0.04090330935630.00243075621218-0.1186841901730.2024199207020.002358694063980.2244682542140.02782798646720.01644737465510.239087504432-0.01142160807230.17654283168423.0692092845-22.83615336619.57004024506
32.95464206760.05165687479780.3601122731642.160100689330.8201830740133.582959553020.01051863571320.137985397775-0.130131564337-0.10665966206-0.1035926705190.2624878069750.213012947502-0.3516844652580.09517248737720.192477873670.0296665727618-0.01201304599780.2122079036580.01360613286480.2203726366598.64202992003-31.519891426725.235067554
47.467931861841.37234749611-3.217696145040.4127405233660.2018428819417.343963902850.0509939483782-0.5224047291120.3379058550340.261443070974-0.006163738549040.08777401552140.5030134341650.144844509319-0.03273129856770.249948860372-0.000849741743975-0.02335369894870.1903198985690.04115174188610.2204271011229.2493912995-36.062478004852.0108327211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 275 )
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 99 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 9 )

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