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- PDB-5c0d: HLA-A02 carrying AQWGPDPAAA -

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Basic information

Entry
Database: PDB / ID: 5c0d
TitleHLA-A02 carrying AQWGPDPAAA
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Marker peptide
KeywordsIMMUNE SYSTEM / IMMUNO / HLA-A02 / 1E6-TCR / Cross-reactivity
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / positive regulation of memory T cell activation / TAP complex binding / negative regulation of acute inflammatory response / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / 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 / CD8 receptor binding / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / endoplasmic reticulum exit site / regulation of protein localization to plasma membrane / beta-2-microglobulin binding / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / TAP binding / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / protection from natural killer cell mediated cytotoxicity / 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 / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / detection of bacterium / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / T cell receptor binding / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / lumenal side of endoplasmic reticulum membrane / regulation of transmembrane transporter activity / positive regulation of cell differentiation / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / wound healing / negative regulation of forebrain neuron differentiation / insulin receptor binding / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / negative regulation of protein catabolic process / MHC class I peptide loading complex / positive regulation of neuron projection development / hormone activity / HFE-transferrin receptor complex
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / molecular replacement / Resolution: 1.68 Å
AuthorsRizkallah, P.J. / Bulek, A.M. / Cole, D.K. / Sewell, A.K.
CitationJournal: J.Clin.Invest. / Year: 2016
Title: Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity.
Authors: Cole, D.K. / Bulek, A.M. / Dolton, G. / Schauenberg, A.J. / Szomolay, B. / Rittase, W. / Trimby, A. / Jothikumar, P. / Fuller, A. / Skowera, A. / Rossjohn, J. / Zhu, C. / Miles, J.J. / ...Authors: Cole, D.K. / Bulek, A.M. / Dolton, G. / Schauenberg, A.J. / Szomolay, B. / Rittase, W. / Trimby, A. / Jothikumar, P. / Fuller, A. / Skowera, A. / Rossjohn, J. / Zhu, C. / Miles, J.J. / Peakman, M. / Wooldridge, L. / Rizkallah, P.J. / Sewell, A.K.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Marker peptide


Theoretical massNumber of molelcules
Total (without water)44,8143
Polymers44,8143
Non-polymers00
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-17 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.840, 81.150, 56.190
Angle α, β, γ (deg.)90.000, 112.320, 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 antigen A*2 / HLA-A02 Heavy Chain


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) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / 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) / References: UniProt: P61769
#3: Protein/peptide Marker peptide


Mass: 983.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium malonate, 0.1M BIS TRIS propane, pH 6.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.68→31.221 Å / Num. all: 49373 / Num. obs: 49373 / % possible obs: 98.8 % / Redundancy: 3.9 % / Rpim(I) all: 0.056 / Rrim(I) all: 0.112 / Rsym value: 0.084 / Net I/av σ(I): 7.595 / Net I/σ(I): 8.7 / Num. measured all: 192943
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.68-1.723.50.6811.11260835700.4880.6811.597.5
1.72-1.773.70.5781.31337535920.3970.5781.999.1
1.77-1.823.80.5071.51312334690.3370.5072.399.3
1.82-1.883.80.4231.81284533390.2880.4232.698.8
1.88-1.943.90.2712.81270732720.180.2714.399.4
1.94-2.013.90.2163.51235131470.1430.2165.198.9
2.01-2.0840.1724.41191730160.1130.1726.498.9
2.08-2.1740.1465.21174129460.0950.1467.698.9
2.17-2.2740.12761114527790.0820.1278.898.3
2.27-2.3840.1265.91068926540.0810.1268.498.4
2.38-2.54.10.1027.21030425400.0650.1021098.4
2.5-2.6640.0918.1981224310.0580.09111.598.4
2.66-2.8440.0788.9908522690.050.07813.499
2.84-3.0740.0758.9831221010.0480.07514.898.5
3.07-3.363.80.05911.5741619460.0390.05916.998.4
3.36-3.763.90.04714692117810.0310.04719.999.1
3.76-4.344.10.04115.8642315690.0250.04121.699.6
4.34-5.314.10.03817552013340.0240.03822.499.3
5.31-7.514.20.0415.4433610400.0250.0421.3100
7.51-31.22140.0321.923135780.0180.032398.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.35 / Cor.coef. Fo:Fc: 0.68 / Cor.coef. Io to Ic: 0.617
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
AMoREphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UTQ

3utq


Resolution: 1.68→31.22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2081 / WRfactor Rwork: 0.165 / FOM work R set: 0.8332 / SU B: 5.179 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1013 / SU Rfree: 0.1043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 2496 5.1 %RANDOM
Rwork0.1715 ---
obs0.1737 46848 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.42 Å2 / Biso mean: 20.449 Å2 / Biso min: 7.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å2-0.42 Å2
2---0.85 Å20 Å2
3---0.64 Å2
Refinement stepCycle: final / Resolution: 1.68→31.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 0 489 3650
Biso mean---29.9 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193380
X-RAY DIFFRACTIONr_bond_other_d0.0020.023021
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.9224601
X-RAY DIFFRACTIONr_angle_other_deg0.8736962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8685405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95823.279183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13215547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.551530
X-RAY DIFFRACTIONr_chiral_restr0.1130.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213904
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02852
X-RAY DIFFRACTIONr_mcbond_it1.0641.0121602
X-RAY DIFFRACTIONr_mcbond_other1.0641.0121601
X-RAY DIFFRACTIONr_mcangle_it1.7191.5092013
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 173 -
Rwork0.295 3386 -
all-3559 -
obs--97.29 %
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)
10.598-0.3170.15872.2566-0.41491.0101-0.01450.0471-0.006-0.0161-0.0412-0.1546-0.02070.08240.05570.0054-0.0061-0.00440.0237-0.00510.034724.00258.63113.069
24.71.64012.08641.20740.97771.44760.02080.1237-0.1894-0.06350.02680.02790.0397-0.0266-0.04760.02850.01020.00010.05280.00760.03930.227-18.513613.0057
31.85681.0039-1.40943.6374-1.91122.86970.017-0.0340.14270.13250.1670.3735-0.0869-0.1765-0.1840.01530.0139-0.00390.0703-0.00940.07240.82981.179825.3293
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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