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- PDB-3uts: 1E6-A*0201-ALWGPDPAAA Complex, Monoclinic -

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Basic information

Entry
Database: PDB / ID: 3uts
Title1E6-A*0201-ALWGPDPAAA Complex, Monoclinic
Components
  • 1E6 TCR Alpha Chain
  • 1E6 TCR Beta Chain
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Insulin
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex / Human Leukocyte antigen / Type I Diabetes / T cell Receptor
Function / homology
Function and homology information


positive regulation of memory T cell activation / negative regulation of NAD(P)H oxidase activity / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of glycogen catabolic process / CD8 receptor binding ...positive regulation of memory T cell activation / negative regulation of NAD(P)H oxidase activity / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of glycogen catabolic process / CD8 receptor binding / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / positive regulation of respiratory burst / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / endoplasmic reticulum exit site / positive regulation of protein autophosphorylation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / Signal attenuation / fatty acid homeostasis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of insulin receptor signaling pathway / negative regulation of lipid catabolic process / detection of bacterium / T cell receptor binding / regulation of protein localization to plasma membrane / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / COPI-mediated anterograde transport / transport vesicle / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / Insulin receptor recycling / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of nitric-oxide synthase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / regulation of transmembrane transporter activity / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / positive regulation of glycolytic process / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / endosome lumen / acute-phase response / cellular response to iron ion / positive regulation of D-glucose import / positive regulation of protein secretion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / positive regulation of cell differentiation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Regulation of insulin secretion / peptide antigen assembly with MHC class II protein complex / insulin receptor binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / wound healing / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / negative regulation of protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / hormone activity
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Insulin / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.712 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Sewell, A.K. / Bulek, A.M.
CitationJournal: Nat.Immunol. / Year: 2012
Title: Structural basis for the killing of human beta cells by CD8(+) T cells in type 1 diabetes.
Authors: Bulek, A.M. / Cole, D.K. / Skowera, A. / Dolton, G. / Gras, S. / Madura, F. / Fuller, A. / Miles, J.J. / Gostick, E. / Price, D.A. / Drijfhout, J.W. / Knight, R.R. / Huang, G.C. / Lissin, N. ...Authors: Bulek, A.M. / Cole, D.K. / Skowera, A. / Dolton, G. / Gras, S. / Madura, F. / Fuller, A. / Miles, J.J. / Gostick, E. / Price, D.A. / Drijfhout, J.W. / Knight, R.R. / Huang, G.C. / Lissin, N. / Molloy, P.E. / Wooldridge, L. / Jakobsen, B.K. / Rossjohn, J. / Peakman, M. / Rizkallah, P.J. / Sewell, A.K.
History
DepositionNov 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Insulin
D: 1E6 TCR Alpha Chain
E: 1E6 TCR Beta Chain
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Insulin
I: 1E6 TCR Alpha Chain
J: 1E6 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,25714
Polymers190,87610
Non-polymers3804
Water1,62190
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Insulin
D: 1E6 TCR Alpha Chain
E: 1E6 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6307
Polymers95,4385
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Insulin
I: 1E6 TCR Alpha Chain
J: 1E6 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6267
Polymers95,4385
Non-polymers1882
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.680, 84.590, 126.280
Angle α, β, γ (deg.)90.000, 90.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules AFBGDIEJ

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC Class I Heavy Chain / MHC class I antigen A*2


Mass: 31951.316 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / 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): Rosetta DE3 / References: UniProt: P61769
#4: Protein 1E6 TCR Alpha Chain


Mass: 22613.066 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) / Strain (production host): Rosetta DE3
#5: Protein 1E6 TCR Beta Chain


Mass: 28026.434 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) / Strain (production host): Rosetta DE3

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Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide Insulin


Mass: 968.063 Da / Num. of mol.: 2
Fragment: Pre-pro-insulin Derived Peptide (UNP residues 15-24)
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 3 types, 94 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 20% w/v PEG3350, 0.2 M sodium citrate, 0.1 M Bis-tris propane, pH 6.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2011 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.712→63.14 Å / Num. all: 53477 / Num. obs: 53477 / % possible obs: 99.4 % / Redundancy: 4.1 % / Rsym value: 0.085 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.712-2.784.20.70611631038940.70699.4
2.78-2.864.20.5841.21623638580.58499.6
2.86-2.944.20.4341.71578137460.43499.5
2.94-3.034.20.3332.21526436360.33399.7
3.03-3.134.20.2492.91490135410.24999.9
3.13-3.244.20.2073.51425534060.20799.7
3.24-3.364.20.1574.71367632670.15799.5
3.36-3.54.20.1315.61328231960.13199.6
3.5-3.664.10.0987.51246730280.09899.7
3.66-3.834.10.0848.71175828920.08499.3
3.83-4.0440.07210.11098927280.07297.7
4.04-4.2940.0611.91029825720.0698.5
4.29-4.5840.05212.9982424360.05298.8
4.58-4.9540.04914937823210.04999.6
4.95-5.4240.04913.8839321170.04999.7
5.42-6.064.10.04913.8793919300.04999.6
6.06-74.20.04814.3709117070.048100
7-8.574.10.03916.8597614540.03999.5
8.57-12.1340.03121.1452611260.03199.3
12.13-63.143.70.03119.823076220.03196.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
GDAdata collection
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.712→63.14 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.2691 / WRfactor Rwork: 0.2012 / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.8222 / SU B: 33.107 / SU ML: 0.324 / SU R Cruickshank DPI: 0.3302 / SU Rfree: 0.3837 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2691 2715 5.1 %RANDOM
Rwork0.2012 ---
obs0.2046 53460 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 182.01 Å2 / Biso mean: 60.0573 Å2 / Biso min: 9.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å2-0.35 Å2
2--3.66 Å20 Å2
3----3.17 Å2
Refinement stepCycle: LAST / Resolution: 2.712→63.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13430 0 21 90 13541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02113842
X-RAY DIFFRACTIONr_bond_other_d0.0010.029466
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.93518802
X-RAY DIFFRACTIONr_angle_other_deg0.744322871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.47451657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.35223.681709
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.932152237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.50315103
X-RAY DIFFRACTIONr_chiral_restr0.090.21942
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02115539
X-RAY DIFFRACTIONr_gen_planes_other00.022972
X-RAY DIFFRACTIONr_mcbond_it2.15828329
X-RAY DIFFRACTIONr_mcbond_other0.47223319
X-RAY DIFFRACTIONr_mcangle_it3.801313454
X-RAY DIFFRACTIONr_scbond_it5.46345513
X-RAY DIFFRACTIONr_scangle_it8.02765348
LS refinement shellResolution: 2.712→2.782 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 174 -
Rwork0.325 3713 -
all-3887 -
obs--100 %
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)
13.99140.9526-0.66422.86631.55585.01-0.14130.62990.1949-0.0951-0.04850.22740.0055-0.59540.18970.0315-0.03090.02120.1572-0.01160.071349.212211.247312.3751
28.0061-5.7335-2.93496.05911.31962.8463-0.1670.23410.23360.24060.36310.1654-0.3725-0.1191-0.19610.1743-0.07470.00150.5155-0.03610.370514.53715.05519.4774
38.50054.6071-3.08686.6096-1.82565.843-0.0287-0.0747-0.13230.5227-0.55580.51230.518-0.53530.58460.2277-0.13520.21960.1367-0.14340.216829.9632.097929.105
45.91991.1766-4.82022.4867-1.478.38140.05180.47020.2061-0.4029-0.10170.1184-0.1391-0.64490.04990.15940.0036-0.03190.158-0.04410.06770.75259.3747-12.8249
57.03161.4007-0.19568.3564-1.069510.11850.07320.33760.03850.106-0.0863-0.1446-0.07080.42980.01310.0733-0.02940.06870.2897-0.02880.0721100.85662.2435-27.4592
68.485-3.1464-1.96822.4150.45256.5036-0.2318-0.5265-0.3722-0.08190.2174-0.02030.87060.65450.01450.20340.04030.05480.1044-0.01030.057377.63280.41527.0685
76.13012.4776-3.26045.1046-3.23118.6493-0.0426-0.5063-0.20720.21040.0731-0.0658-0.04210.9966-0.03060.17360.1379-0.03570.3974-0.14750.1261103.41190.4531-10.1944
84.6625-1.16241.55854.17221.9815.449-0.2083-0.5935-0.1616-0.0190.08590.323-0.2658-0.60140.12240.11240.1033-0.08710.1521-0.04010.109555.222340.295950.9855
910.33824.60375.47184.29192.226310.34340.1139-0.9414-0.61330.2635-0.24810.59331.3119-1.43730.13430.36020.12550.0510.9702-0.00290.905419.970237.251646.0196
107.6482-4.83922.26717.4248-2.19065.08830.01130.1018-0.079-0.2382-0.09810.5393-0.1991-0.42490.08690.29190.1184-0.21140.1914-0.10420.270135.416649.478534.6755
113.0427-0.64392.26731.4285-1.9069.4698-0.0343-0.3359-0.18450.2718-0.1582-0.0148-0.0593-0.45690.19250.1345-0.03520.00390.1407-0.02890.099177.023341.640575.9443
125.88480.8486-0.38643.82030.00969.71170.094-0.66370.2522-0.0933-0.13980.1098-0.3693-0.17560.04580.09110.001-0.05420.2466-0.00690.0779107.020247.797390.7779
138.87062.9051.89383.00340.15634.2985-0.09920.31550.35390.1833-0.0606-0.203-0.57280.15640.15980.15990.0246-0.05150.06370.02870.065984.208949.739855.7642
144.3185-1.93642.17466.3929-3.12847.82420.05740.10760.0681-0.1234-0.063-0.01650.06760.49020.00550.0966-0.05280.01820.0727-0.03190.0716110.114348.514373.3975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D3 - 110
6X-RAY DIFFRACTION5D115 - 200
7X-RAY DIFFRACTION6E1 - 110
8X-RAY DIFFRACTION7E115 - 241
9X-RAY DIFFRACTION8F1 - 180
10X-RAY DIFFRACTION8H1 - 9
11X-RAY DIFFRACTION9F181 - 276
12X-RAY DIFFRACTION10G0 - 99
13X-RAY DIFFRACTION11I3 - 110
14X-RAY DIFFRACTION12I115 - 200
15X-RAY DIFFRACTION13J1 - 110
16X-RAY DIFFRACTION14J115 - 241

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