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- PDB-5c0e: HLA-A02 carrying YLGGPDFPTI -

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Basic information

Entry
Database: PDB / ID: 5c0e
TitleHLA-A02 carrying YLGGPDFPTI
Components
  • Beta-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


positive regulation of memory T cell activation / 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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of memory T cell activation / 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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / 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 / detection of bacterium / T cell receptor binding / : / : / 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 / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / 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 / 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 / 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 / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
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 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
BROMIDE ION / 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: 1.491 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
Revision 1.4Oct 23, 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: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Marker peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,75636
Polymers45,1163
Non-polymers3,64033
Water7,044391
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint86 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.070, 79.740, 57.000
Angle α, β, γ (deg.)90.000, 115.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2 / HLA-A02 Heavy Chain


Mass: 32082.512 Da / Num. of mol.: 1 / Fragment: 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


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: 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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Marker peptide


Mass: 1154.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 424 molecules

#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M TRIS pH8, 25% PEG 4000, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.49→31.294 Å / Num. all: 72820 / Num. obs: 72820 / % possible obs: 99 % / Redundancy: 3.9 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.113 / Rsym value: 0.085 / Net I/av σ(I): 5.946 / Net I/σ(I): 12.2 / Num. measured all: 285952
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.49-1.5341.0740.42111253290.6171.0742.398.4
1.53-1.5740.8410.62061952130.4860.8412.998.7
1.57-1.6240.6780.72018850890.3920.6783.498.8
1.62-1.6740.5670.91946949150.3280.5674.198.8
1.67-1.7240.4661.11909448260.2680.466599.2
1.72-1.783.90.3591.41837646540.2120.3596.199.1
1.78-1.8540.2791.81762244550.1630.2797.699.3
1.85-1.933.90.2112.51696643060.1280.2119.299.3
1.93-2.013.90.1563.31609541340.0950.15611.698.7
2.01-2.113.90.13141522139370.0790.13113.498.8
2.11-2.223.90.1035.21448837480.0630.10315.798.2
2.22-2.363.90.08961366335460.0570.08917.299.1
2.36-2.523.90.0747.51302333690.050.07419.199.9
2.52-2.723.80.0648.91204631670.0470.0642199.9
2.72-2.9840.05111.31148028810.0370.0512499.9
2.98-3.3340.04114.21061726410.030.04127.299.9
3.33-3.8540.03517.2922823050.0260.03530.699.8
3.85-4.723.90.03318.5768619640.0240.03332.799.2
4.72-6.673.90.03217.7598215250.0230.03231.699.6
6.67-31.2943.60.03217.429778160.0250.03230.694.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 30.29 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å31.29 Å
Translation2.5 Å31.29 Å

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UTQ

3utq


Resolution: 1.491→31.29 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.1522 / FOM work R set: 0.8835 / SU B: 2.558 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0645 / SU Rfree: 0.0649 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1786 3669 5 %RANDOM
Rwork0.1558 ---
obs0.157 69115 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.15 Å2 / Biso mean: 19.601 Å2 / Biso min: 7.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å2-0.38 Å2
2---0.33 Å2-0 Å2
3---0.59 Å2
Refinement stepCycle: final / Resolution: 1.491→31.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 236 391 3809
Biso mean--35.85 32.04 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193630
X-RAY DIFFRACTIONr_bond_other_d0.0020.023376
X-RAY DIFFRACTIONr_angle_refined_deg2.3591.9624845
X-RAY DIFFRACTIONr_angle_other_deg0.99237786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6455414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19322.919185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5215562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7241533
X-RAY DIFFRACTIONr_chiral_restr0.1240.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213983
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02880
X-RAY DIFFRACTIONr_mcbond_it1.2160.8691620
X-RAY DIFFRACTIONr_mcbond_other1.2160.8691619
X-RAY DIFFRACTIONr_mcangle_it2.0511.2932046
LS refinement shellResolution: 1.491→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 259 -
Rwork0.244 5044 -
all-5303 -
obs--98.08 %
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)
10.73910.1437-0.00221.67070.51010.83970.0451-0.04290.0130.1043-0.03970.10930.0266-0.0471-0.00540.0121-0.00270.01270.00580.00160.0175-0.0195-8.647227.5373
20.1964-0.28580.3481.1528-2.20455.1130.05990.06760.0384-0.0378-0.02110.0131-0.159-0.0358-0.03880.06390.01230.01090.05150.00150.040911.493917.74665.5844
33.36391.3067-0.17733.74080.31961.0575-0.11220.1057-0.1641-0.28640.1952-0.48170.02210.1414-0.08310.0359-0.00270.04370.0371-0.02730.070621.997-1.837312.639
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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