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- PDB-6uk4: Complex of T cell Receptor with HHAT Neoantigen Peptide KQWLVWLFL... -

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Basic information

Entry
Database: PDB / ID: 6uk4
TitleComplex of T cell Receptor with HHAT Neoantigen Peptide KQWLVWLFL 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 / Hedgehog ligand biogenesis / 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 / 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 / Modulation by Mtb of host immune system / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / 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 / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / negative regulation of neuron projection development / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / endoplasmic reticulum membrane / Neutrophil degranulation / 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: 2.7 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 1.5Nov 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
D: 302 TIL T cell receptor alpha chain
E: 302 TIL T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)96,4385
Polymers96,4385
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)45,1143
Polymers45,1143
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-19 kcal/mol
Surface area19190 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 area4450 Å2
ΔGint-25 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.310, 86.507, 238.780
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


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, 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: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1 M sodium citrate, pH 6.3, 7.5% PEG6000, 0.2 M lithium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2019
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 35931 / % possible obs: 99 % / Redundancy: 7.8 % / Biso Wilson estimate: 63.92 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.042 / Rrim(I) all: 0.121 / Net I/σ(I): 16
Reflection shellResolution: 2.69→2.74 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1672 / CC1/2: 0.908 / Rpim(I) all: 0.195 / Rrim(I) all: 0.539 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.11.1model building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1TVH, 5JZI, & 5C0B

1tvh

5jzi

5c0b


Resolution: 2.7→49.47 Å / SU ML: 0.3996 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9451
RfactorNum. reflection% reflection
Rfree0.2522 1949 5.58 %
Rwork0.2196 --
obs0.2214 34958 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 73.93 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6728 0 0 0 6728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00426917
X-RAY DIFFRACTIONf_angle_d0.73899399
X-RAY DIFFRACTIONf_chiral_restr0.0486981
X-RAY DIFFRACTIONf_plane_restr0.00351229
X-RAY DIFFRACTIONf_dihedral_angle_d23.49662551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.37651300.35642206X-RAY DIFFRACTION95.27
2.77-2.840.38151380.31742321X-RAY DIFFRACTION99.19
2.84-2.930.38951370.32612318X-RAY DIFFRACTION99.19
2.93-3.020.29151380.30212339X-RAY DIFFRACTION99.48
3.02-3.130.32351370.28392317X-RAY DIFFRACTION99.8
3.13-3.250.31511370.2932335X-RAY DIFFRACTION99.64
3.25-3.40.3381380.28322318X-RAY DIFFRACTION97.5
3.4-3.580.28491390.26462354X-RAY DIFFRACTION99.76
3.58-3.810.24731400.22692373X-RAY DIFFRACTION100
3.81-4.10.24671390.21332367X-RAY DIFFRACTION100
4.1-4.510.21271410.18142374X-RAY DIFFRACTION99.96
4.51-5.160.18131400.16752382X-RAY DIFFRACTION98.98
5.16-6.50.23941450.19632452X-RAY DIFFRACTION100
6.5-49.470.20991500.16862553X-RAY DIFFRACTION99.34
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)
12.04947131872-0.03722438331910.3763376577772.36370595213-0.3121906238592.63477948087-0.1964768228070.0864954829101-0.2332755076690.074186062810.0409286751986-0.04761568277420.734594887535-0.02062899334720.1780309224181.00849261413-0.03324965696730.2442679447070.383466511118-0.01071985695250.667736327298-60.922230159433.290909611336.3912811692
23.20294640928-0.52926783930.02870759286253.07955862379-1.813524298023.669910082950.1485136528370.183185112047-0.355798753903-0.711334122090.01406230757170.1374262552730.314332701235-0.134787581126-0.1709898003781.25406925773-0.06100671578570.1533648821420.472321741052-0.01952516840090.584477452255-71.75106372465.5195212539855.462463237
34.471919831831.439941744740.5239270112342.286683120710.1864119010550.771908379618-0.2815372591150.0813456395283-0.214871793239-0.3784353087140.2658313435640.345518975740.372423190733-0.2847147473510.03370280160651.14915939197-0.1986816083450.2393302529450.5539848056280.03375688615740.870022641678-83.24104887619.132886066541.7753774343
41.720721814310.412426024081-0.2055287879071.002574883450.704243097746.929752240550.0589239962230.368040595643-0.3359071019920.4904509552480.468406438115-0.2287561543051.061942227040.343021019538-0.4841476491530.8403033003210.1584489632170.2134257239250.439411622325-0.02413910114540.661356724439-57.23649019739.415408905132.2600323025
55.541346182463.08578671787-1.032337020754.244515418810.3703525633064.61655533241-0.0434227263632-0.177340573304-0.20088756210.448493265565-0.0278109503638-0.1843863666150.2745788361250.7547399844440.06858367814620.4022203891950.128514167354-0.03402070964220.5149834887760.01951563853330.513949089123-42.5907078619-27.223547279434.5727229694
66.062510870620.2351645531860.08606443950894.112026586480.5674557259123.678156039380.0301926494013-0.6211469603770.600454131768-0.4502398387980.132680897889-0.17430263337-0.9325324539780.812241647482-0.1280721577660.730284284329-0.319408400090.02424407310250.917728744026-0.1375135179650.725594349693-27.85512929770.3335616875418.829782613
71.562169079010.09262081000770.1142879655816.52516076613-0.9661117584324.35340095345-0.04108046784270.3241763694750.2422051942590.0160389271261-0.02587100277890.256510743270.20746974688-0.2402326747330.08827916010690.232326203243-0.00183489650914-0.006012252867660.5739941035560.01910483152340.510452545557-57.4961534892-27.188762353916.8442833218
87.562150892430.0658280920172-0.9596427054942.66348192992-0.3136059154993.208931257330.259942156516-0.3727328649820.541385248084-0.0696098857555-0.07666667044670.21446686869-0.4678812034120.185950152474-0.1497758999680.392834636808-0.0958770714275-0.008019911684830.4601625511680.07094960729280.502982092651-37.0191570663-7.307809798346.0415393933
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 )
5X-RAY DIFFRACTION5chain 'D' and (resid 3 through 114 )
6X-RAY DIFFRACTION6chain 'D' and (resid 115 through 204 )
7X-RAY DIFFRACTION7chain 'E' and (resid 2 through 115 )
8X-RAY DIFFRACTION8chain 'E' and (resid 116 through 245 )

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