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- PDB-3utq: Human HLA-A*0201-ALWGPDPAAA -

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Basic information

Entry
Database: PDB / ID: 3utq
TitleHuman HLA-A*0201-ALWGPDPAAA
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Insulin
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex / Human Leukocyte antigen / Type I Diabetes
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: 1.67 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 6, 2024Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Insulin


Theoretical massNumber of molelcules
Total (without water)44,7993
Polymers44,7993
Non-polymers00
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-21 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.100, 81.150, 56.550
Angle α, β, γ (deg.)90.000, 112.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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.: 1 / 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.: 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): Rosetta DE3 / References: UniProt: P61769
#3: Protein/peptide Insulin


Mass: 968.063 Da / Num. of mol.: 1
Fragment: Pre-pro-insulin Derived Peptide (UNP residues 15-24)
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 20% w/v PEG3350, 0.2 M potassium/sodium tartrate, 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: 1.67→45.587 Å / Num. all: 50250 / Num. obs: 50250 / % possible obs: 98.1 % / Redundancy: 4 % / Rsym value: 0.05 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.67-1.7140.571.41452035940.5794.8
1.71-1.764.10.471.71493036180.4798.5
1.76-1.814.10.3712.11447135170.37199.1
1.81-1.874.10.3262.41419134440.32698.7
1.87-1.933.90.19641287832660.19697.4
1.93-24.10.2113.71308632200.21198.9
2-2.074.10.136.11288931390.1399
2.07-2.164.10.1087.31236030110.10899.2
2.16-2.253.90.0987.91073627370.09894.1
2.25-2.3640.0977.91037026130.09794.3
2.36-2.4940.06611.91051926280.06699.4
2.49-2.6440.05414.6984324670.05498.7
2.64-2.8240.04318941523570.04399.3
2.82-3.0540.03620.4865821820.03699.3
3.05-3.343.90.02626.4788020120.02699.2
3.34-3.733.90.02328.9708618010.02398.8
3.73-4.314.20.01739.2671016130.01799.4
4.31-5.284.20.01442.4568413640.01499.9
5.28-7.474.10.01641.4444510780.016100
7.47-45.5873.90.01441.723135890.01497.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
GDAdata collection
xia2data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→45.587 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.868 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 2545 5.1 %RANDOM
Rwork0.195 ---
obs0.1975 50142 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: 71.95 Å2 / Biso mean: 23.8571 Å2 / Biso min: 7.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å2-1.28 Å2
2---0.82 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.67→45.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 0 525 3685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213255
X-RAY DIFFRACTIONr_bond_other_d0.0010.022229
X-RAY DIFFRACTIONr_angle_refined_deg2.1611.9234422
X-RAY DIFFRACTIONr_angle_other_deg1.07935359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3695383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.37723.161174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.48215521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.651528
X-RAY DIFFRACTIONr_chiral_restr0.1420.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02721
X-RAY DIFFRACTIONr_mcbond_it1.1211.51925
X-RAY DIFFRACTIONr_mcbond_other0.41.5774
X-RAY DIFFRACTIONr_mcangle_it1.80823100
X-RAY DIFFRACTIONr_scbond_it2.9831330
X-RAY DIFFRACTIONr_scangle_it4.5984.51322
LS refinement shellResolution: 1.67→1.714 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 188 -
Rwork0.246 3397 -
all-3585 -
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)
10.7689-0.02780.28572.5562-0.61571.2822-0.01630.0532-0.03630.0882-0.0337-0.25620.00080.06820.050.0042-0.0024-0.00720.0213-0.0080.036123.96979.078613.364
26.82242.53273.45822.08841.63231.9340.15990.1481-0.40740.00420.008-0.02440.09590.0024-0.16790.05370.0026-0.00590.064-0.00820.04110.2924-18.183112.8473
33.3751.0182-1.8123.8105-1.84333.5402-0.0632-0.14880.06940.1010.18190.3703-0.0105-0.1243-0.11860.00770.02030.010.07230.01320.03770.86151.03225.3949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99

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