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- PDB-6uk2: Complex of T cell Receptor with HHAT Wild Type Peptide KQWLVWLLL ... -

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Basic information

Entry
Database: PDB / ID: 6uk2
TitleComplex of T cell Receptor with HHAT Wild Type Peptide KQWLVWLLL Presented by HLA-A206
Components
  • 302 TIL T cell receptor alpha chain
  • 302 TIL T cell receptor beta chain
  • Beta-2-microglobulin
  • MHC class I antigen
  • Protein-cysteine N-palmitoyltransferase HHAT
KeywordsIMMUNE SYSTEM / Neoantigen / Peptide/MHC / T cell receptor
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: 3.13880812156 Å
AuthorsDevlin, J.R. / Baker, B.M.
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 4, 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 30, 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
D: 302 TIL T cell receptor alpha chain
E: 302 TIL T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)96,4045
Polymers96,4045
Non-polymers00
Water00
1
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-17 kcal/mol
Surface area19220 Å2
MethodPISA
2
D: 302 TIL T cell receptor alpha chain
E: 302 TIL T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)51,3242
Polymers51,3242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-28 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.357, 85.932, 240.728
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein MHC class I antigen / HLA-A*02:06


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 / Hedgehog acyltransferase / Melanoma antigen recognized by T-cells 2 / MART-2 / Skinny hedgehog protein 1


Mass: 1199.505 Da / Num. of mol.: 1 / Fragment: Neoantigen peptide (UNP residues 68-76) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q5VTY9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#4: Protein 302 TIL T cell receptor alpha chain


Mass: 23541.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 DE3
#5: Protein 302 TIL T cell receptor beta chain


Mass: 27783.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 DE3
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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1 M sodium citrate, pH 6.3, 8.5% PEG6000, 0.20 M lithium nitrate

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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: Jun 20, 2019
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: 3.13→50 Å / Num. obs: 23820 / % possible obs: 98.5 % / Redundancy: 8.2 % / Biso Wilson estimate: 95.6142780273 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.279 / Rpim(I) all: 0.101 / Rrim(I) all: 0.297 / Net I/σ(I): 8.2
Reflection shellResolution: 3.13→3.18 Å / Redundancy: 7.3 % / Rmerge(I) obs: 2.135 / Mean I/σ(I) obs: 2 / Num. unique obs: 1195 / CC1/2: 0.687 / Rpim(I) all: 0.816 / Rrim(I) all: 2.29 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575model building
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1TVH, 5JZI, & 5C0B

1tvh

5jzi

5c0b


Resolution: 3.13880812156→42.297557939 Å / SU ML: 0.480904895823 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.7867395997
RfactorNum. reflection% reflection
Rfree0.259935780929 1906 8.39166996874 %
Rwork0.228723986678 --
obs0.231293791938 22713 93.9446581462 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 96.387439635 Å2
Refinement stepCycle: LAST / Resolution: 3.13880812156→42.297557939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6722 0 0 0 6722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004805460677866910
X-RAY DIFFRACTIONf_angle_d0.8447757628699390
X-RAY DIFFRACTIONf_chiral_restr0.0633831277826982
X-RAY DIFFRACTIONf_plane_restr0.0042375669691227
X-RAY DIFFRACTIONf_dihedral_angle_d21.26536260092549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.13881-3.21730.4767804490121200.3918912214931322X-RAY DIFFRACTION83.6912362159
3.2173-3.30420.3499534250671230.3656334890521356X-RAY DIFFRACTION88.5628742515
3.3042-3.40140.3472619423281330.3106893020911411X-RAY DIFFRACTION90.7168037603
3.4014-3.51120.3513951168221260.3035177658681419X-RAY DIFFRACTION92.1288014311
3.5112-3.63660.3347337936941250.2871728181741334X-RAY DIFFRACTION85.7226792009
3.6366-3.78210.3597375346441180.3095073564651320X-RAY DIFFRACTION83.7995337995
3.7821-3.95410.3002222640161370.2690274265961504X-RAY DIFFRACTION96.359365825
3.9541-4.16240.2917167902271410.2441864669271529X-RAY DIFFRACTION97.775175644
4.1624-4.42290.2374111370851440.216374406521553X-RAY DIFFRACTION99.1238317757
4.4229-4.7640.2361611604931440.1904936698181574X-RAY DIFFRACTION99.4212962963
4.764-5.24260.2408319120371410.1971989144921553X-RAY DIFFRACTION98.3739837398
5.2426-5.99940.2506200082931490.202991750491607X-RAY DIFFRACTION99.7727272727
5.9994-7.55160.2490843802841490.2202927768891615X-RAY DIFFRACTION99.6610169492
7.5516-42.29750.1896513590621560.186999146731710X-RAY DIFFRACTION99.1498405951
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)
13.0941793437-0.600871731948-0.935717029023.715264970690.04441550543455.11548084613-0.018664056234-0.1312324213430.235003963185-0.089139910530.138389859882-0.194033577696-0.44770125930.152285702884-0.1019932072210.7421283543740.0436099362034-0.0763239568820.478896231564-0.004368554260720.7638110572950.04064734704838.31067340333-36.6617933459
26.212176304590.596365290754-0.114857062195.60477802362-2.372870116885.043683402680.28409103253-0.2614975906080.5176445193770.532779798735-0.165303582880.411411518328-0.310349769718-0.149344070143-0.1306220738690.813675615114-0.01237021393290.03560610263170.4948302415620.001873159904440.569150809085-11.511795190935.4157496196-55.8402800201
38.19115910628-0.1630101889443.327491394753.67475970133-0.3525574152595.72480167482-0.125818897061-0.1950340772250.03656690333790.3599544267540.1026567617010.419573111358-0.00250981314883-0.7444498583490.07223347097020.8615560148940.09310025641020.1286355440540.7279808859140.08237296065030.79576022746-22.817261029521.7714270711-41.8967743364
49.04010781262-3.635545902651.729465715864.07824536135-0.964000788067.471832971110.331153681540.4388322226950.248398019263-0.770832096636-0.455058165945-0.3597120297390.09171974837130.9880718335190.130940609010.570118436540.0315590274920.1323046180970.6332049256960.02199195726350.664563655249-44.492282449369.3100491715-34.7087240475
51.854965189280.351821482840.04255336059343.57906565833-0.5341333255975.614500616520.1446453558670.402941787963-0.470587375809-0.393113105576-0.4527452633360.3291235896020.7745440807880.9732288616770.2857860509150.8567084078530.348693971441-0.007447545845761.07302018038-0.1398029422120.950150702605-27.66969018542.6094627663-19.1084328198
66.48329603788-0.3330020418651.458118366158.97679336492-3.263940617568.7379359359-0.107272505812-0.386805750497-0.2126728224120.1154272240760.1186051817220.314548105862-0.0691064522885-0.412424266373-0.009389284542020.441880142532-0.02045744610490.02224374168950.601938489341-0.003250566605180.589277069116-58.972461247669.1598518713-16.4127990546
79.336163199652.019222750120.9895017466943.52196487422-0.07562925086653.060810203650.352289089435-0.0351685998981-0.5931826911860.271892551399-0.07669940107640.1614644258520.2643118964960.161235910051-0.2758542862340.6539610376730.137007286601-0.02938438459180.5760386511390.0918158762190.557730775034-36.868856424150.0589260403-5.95355634223
82.316759675180.382105761974-0.8525445433951.475197737012.263403116544.306953584460.185476490177-0.215078520770.4227829691050.2190333698960.372874821893-0.0964432608921-1.49644666070.563581888276-0.46276876571.2611238091-0.153537455056-0.09507446857540.4874640540360.1212467183861.145658724194.244451938242.47031422491-32.6396562481
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 'D' and (resid 3 through 114 )
5X-RAY DIFFRACTION5chain 'D' and (resid 115 through 204 )
6X-RAY DIFFRACTION6chain 'E' and (resid 2 through 115 )
7X-RAY DIFFRACTION7chain 'E' and (resid 116 through 245 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 9 )

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