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- PDB-6uz1: Noncanonical binding of single-chain A6 TCR variant S3-4 in compl... -

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Basic information

Entry
Database: PDB / ID: 6uz1
TitleNoncanonical binding of single-chain A6 TCR variant S3-4 in complex with Tax/HLA-A2
Components
  • (T cell receptor, ...) x 2
  • Beta-2-microglobulin
  • LEU-LEU-PHE-GLY-TYR-PRO-VAL-TYR-VAL
  • MHC class I antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / single-chain T cell receptor / peptide Major Histocompatibility complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated activation of host NF-kappaB cascade / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / antigen processing and presentation of peptide antigen via MHC class I / regulation of mRNA stability / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated activation of host NF-kappaB cascade / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / antigen processing and presentation of peptide antigen via MHC class I / regulation of mRNA stability / 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 / lumenal side of endoplasmic reticulum membrane / 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 / 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 / SH3 domain binding / 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 / cellular response to lipopolysaccharide / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / positive regulation of DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / DNA binding / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
HTLV Tax / HTLV Tax / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 ...HTLV Tax / HTLV Tax / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Major histocompatibility complex, class I, A / MHC class I antigen / Protein Tax-1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsMa, J. / Singh, N.K.
CitationJournal: Biochemistry / Year: 2020
Title: An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding Modes.
Authors: Singh, N.K. / Alonso, J.A. / Harris, D.T. / Anderson, S.D. / Ma, J. / Hellman, L.M. / Rosenberg, A.M. / Kolawole, E.M. / Evavold, B.D. / Kranz, D.M. / Baker, B.M.
History
DepositionNov 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: LEU-LEU-PHE-GLY-TYR-PRO-VAL-TYR-VAL
F: MHC class I antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: LEU-LEU-PHE-GLY-TYR-PRO-VAL-TYR-VAL
I: T cell receptor, alpha chain
J: T cell receptor, beta chain
D: T cell receptor, alpha chain
E: T cell receptor, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,08312
Polymers138,69210
Non-polymers3902
Water1448
1
A: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: LEU-LEU-PHE-GLY-TYR-PRO-VAL-TYR-VAL
D: T cell receptor, alpha chain
E: T cell receptor, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5416
Polymers69,3465
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: MHC class I antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: LEU-LEU-PHE-GLY-TYR-PRO-VAL-TYR-VAL
I: T cell receptor, alpha chain
J: T cell receptor, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5416
Polymers69,3465
Non-polymers1951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)236.650, 236.650, 63.146
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
DetailsAn assembly that is closer to the conventional one may be generated by using chains A, B and C of the primary asymmetric unit, along with chains E and D generated by SymOp 1_554; or by using chains F, G and H of the primary asymmetric unit, along with chains I and J generated by SymOp 1_556

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Components

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Protein , 2 types, 4 molecules AFBG

#1: Protein MHC class I antigen, A-2 alpha chain


Mass: 31854.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B8RNS7, UniProt: A0A140T913*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide LEU-LEU-PHE-GLY-TYR-PRO-VAL-TYR-VAL


Mass: 1070.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P14079*PLUS

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T cell receptor, ... , 2 types, 4 molecules IDJE

#4: Protein T cell receptor, alpha chain


Mass: 11995.190 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein T cell receptor, beta chain


Mass: 12547.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 10 molecules

#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.68 Å3/Da / Density % sol: 66.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10%w/v Polyethylene glycol 20,000, 100mMMES, 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: MAR CCD 130 mm / Detector: CCD / Date: Jul 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 37072 / % possible obs: 99.4 % / Redundancy: 11 % / Biso Wilson estimate: 81.4 Å2 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.087 / Rrim(I) all: 0.289 / Net I/σ(I): 14.7
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.978 / Num. unique obs: 1889 / CC1/2: 0.803 / Rpim(I) all: 0.648 / Rrim(I) all: 2.082 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FTV

4ftv


Resolution: 3.14→44.72 Å / SU ML: 0.4445 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4977
RfactorNum. reflection% reflection
Rfree0.2394 2003 5.62 %
Rwork0.1891 --
obs0.192 35632 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 103.87 Å2
Refinement stepCycle: LAST / Resolution: 3.14→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9720 0 24 8 9752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00189999
X-RAY DIFFRACTIONf_angle_d0.468413568
X-RAY DIFFRACTIONf_chiral_restr0.0391413
X-RAY DIFFRACTIONf_plane_restr0.0031769
X-RAY DIFFRACTIONf_dihedral_angle_d11.74683657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.220.37011320.3372253X-RAY DIFFRACTION94.79
3.22-3.30.34891400.27452404X-RAY DIFFRACTION99.57
3.3-3.40.29961400.25992381X-RAY DIFFRACTION99.37
3.4-3.510.30121420.24112393X-RAY DIFFRACTION99.61
3.51-3.640.27861410.22212362X-RAY DIFFRACTION99.96
3.64-3.780.29861390.21082394X-RAY DIFFRACTION99.45
3.78-3.950.26091410.20592423X-RAY DIFFRACTION99.69
3.95-4.160.24711430.18132391X-RAY DIFFRACTION99.96
4.16-4.420.21571460.16032391X-RAY DIFFRACTION100
4.42-4.760.19321410.14242419X-RAY DIFFRACTION99.96
4.76-5.240.18111490.14472433X-RAY DIFFRACTION100
5.24-60.19491440.1652412X-RAY DIFFRACTION100
6-7.550.24181520.20192449X-RAY DIFFRACTION100
7.56-44.720.231530.17632524X-RAY DIFFRACTION99.37
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)
12.082133777240.638210424248-0.04306322436875.14048989203-1.278515069092.873572650510.09457339464440.0543658341562-0.0230620587122-0.204359309971-0.181516330361-0.2857062567370.03267009024720.236147073530.06514931132410.514154935195-0.275262372924-0.03363063423690.770356099846-0.02059920835890.451011643988-46.37447790878.689897206-17.7414784759
24.27345159754-3.8380134788-3.818846803897.062195438882.929115556616.161930585190.2897626630590.198324072553-0.02809833081980.293980674608-0.1400557114320.173239039466-0.434640919286-0.254672087699-0.1764154235520.845770774055-0.421893252134-0.07845521936590.917811544740.08592508147760.425722212717-58.510960646688.479217435714.1101178608
31.747915290.634446366260.8164641134411.274841817860.8575624364080.8458159458470.124507528899-0.3533807112690.03677984777570.725463271109-0.244900761228-0.575266960193-0.3453347791020.5976560680750.002737902939030.965495363906-0.832550962625-0.2265790902941.1857383111-0.0213276415410.591404067548-39.135466901793.95198555383.51032201643
45.436474155111.38382773558-1.96812150473.499318662360.6938098622832.377470557630.106072240971.45346125531-0.192086001318-1.15917356112-0.324408454253-0.227882487175-0.005164252144541.329903574590.3400544589020.624423814044-0.238612207850.08228748801381.11436989407-0.04504736535270.626522295434-45.373602834775.9520032206-25.7877610656
53.22956938407-0.300554200398-1.097983903081.834309685960.1795678377112.84452180526-0.291122858661-0.193827777444-0.06326924644970.3698500410620.06432320032510.2109819621910.931288168995-0.4706754364470.2111568622261.42988408526-0.5069949548260.08388736148710.919727132076-0.112067858970.579087875881-75.266900755654.309287860332.6358834986
66.94284222326-3.607642601065.035075128874.99585505627-4.298694896164.86497868579-0.0304511988062-0.1718316814130.4383808508790.435300808040.03556568374820.246125883388-0.69115610354-0.5522421869510.04161990337261.22978238557-0.1432986931130.1021107457380.980958361253-0.1153790657650.573496488322-83.268938468568.15314227430.710204625525
76.29372030040.2981231370092.430314762354.252107141722.809716654846.842561942280.4206697603030.0307146320307-0.2845080619060.406743053667-0.3946227185210.4204118175030.570137247198-0.8118357852950.03199408417281.04114714727-0.5152375368290.0427007144941.16153802091-0.1146138546350.738624602596-91.518775005849.787819578911.4628121982
83.09712522163-1.45276575793-3.095375210480.7379792967651.317709979623.40868437454-0.247946010755-1.68893740801-0.3427376917052.00682135994-0.2394444368540.5437130407210.916219273920.9172995184550.5285618199332.04363596137-0.4459452802630.05539559536471.039364509430.03996483882240.65479782827-72.551177936652.773817953240.8139463922
93.918881201450.4229523364890.1692544859446.569891358271.526294543264.363980657850.005090679926230.0416716946783-0.3379097529610.5950516841660.185987819570.04660956334690.507437794460.0273225858542-0.1462068344161.23493242197-0.2311526658270.02388779866290.5824939007140.008450406794890.612038522195-70.115923477929.28652196011.82221784325
109.04659795126-5.04227561532-1.994756043399.89560044012.628259393713.74670318940.191992477078-0.1902036910630.1713001027750.1305815971310.0804282480867-1.1036178237-0.145054623810.612622402356-0.27242955720.888567307348-0.275465648637-0.05354145944560.629912805515-0.001727865243210.663272737269-54.570193012844.7830003921-5.18938271464
116.92811656243-0.6836773048454.96334774482.65914050785-0.1577510290783.6065135988-0.377724843019-0.4076744394470.1411578864940.4961227789650.215681735282-0.558122176875-0.1175365806281.465355326940.07450571271040.860748203821-0.137200648849-0.2072072310171.99429427280.1110594240640.832477048128-22.677826707969.356369173413.111979625
128.27976681331-2.302002890532.576683144887.26116229645-2.017934669687.02736947523-0.505986544271-0.979793123791-1.218195785740.9084148154820.3692022467690.4224299157960.6730925026730.4900505323660.09347210512170.9712106773510.1200650410790.0851483656170.9993254143420.2169436714650.704510569514-40.428169720957.346765040720.7971434479
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 'F' and (resid 1 through 180 )
6X-RAY DIFFRACTION6chain 'F' and (resid 181 through 275 )
7X-RAY DIFFRACTION7chain 'G' and (resid 0 through 99 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 9 )
9X-RAY DIFFRACTION9chain 'I' and (resid 2 through 117 )
10X-RAY DIFFRACTION10chain 'J' and (resid 2 through 117 )
11X-RAY DIFFRACTION11chain 'D' and (resid 2 through 115 )
12X-RAY DIFFRACTION12chain 'E' and (resid 3 through 116 )

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