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- PDB-5c0f: HLA-A02 carrying RQWGPDPAAV -

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Basic information

Entry
Database: PDB / ID: 5c0f
TitleHLA-A02 carrying RQWGPDPAAV
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Marker peptide
KeywordsIMMUNE SYSTEM / IMMUNO / HLA-A02 / 1E6-TCR
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 / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / 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 / endoplasmic reticulum exit site ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / 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 / 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 / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin 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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / antibacterial humoral response / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / 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: 1.463 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,96829
Polymers45,0593
Non-polymers1,90926
Water8,233457
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-11 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.360, 79.780, 56.970
Angle α, β, γ (deg.)90.000, 115.700, 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: 1097.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 483 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M TRIS, pH 8, 20% PEG 8000, 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: 1.46→42.841 Å / Num. all: 77814 / Num. obs: 77814 / % possible obs: 99.4 % / Redundancy: 4 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.069 / Rsym value: 0.049 / Net I/av σ(I): 13 / Net I/σ(I): 14.7 / Num. measured all: 313592
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
1.46-1.540.5451.42329557620.3620.5452.3100
1.5-1.5440.4471.72275256260.2960.4472.799.9
1.54-1.594.10.3482.22217354600.2310.3483.599.9
1.59-1.644.10.2962.62157753110.1940.2964.199.9
1.64-1.694.10.2393.32083551240.1590.239599.9
1.69-1.754.10.19342028449820.1310.1936.199.9
1.75-1.814.10.1525.11966648210.1020.1527.699.8
1.81-1.8940.1226.41870846300.0830.1229.299.6
1.89-1.9740.0978.11737743580.0660.09711.999.3
1.97-2.0740.07410.51637141430.0510.07414.897.4
2.07-2.183.90.05913.11555539700.0410.05917.597.4
2.18-2.313.90.05214.71459537370.0350.05220.798.1
2.31-2.473.90.04416.81400835590.0310.04423.399.2
2.47-2.673.90.03819.31308733490.0280.03826.699.7
2.67-2.9340.03221.81229830760.0240.03230.599.7
2.93-3.274.20.02725.31174328020.0190.02736100
3.27-3.784.20.02328.61039525010.0150.02341.7100
3.78-4.634.20.02131.6869020800.0140.02146.299.8
4.63-6.544.10.0231.1671016250.0130.0245.299.8
6.54-42.8413.90.0231.834738980.0140.0244.498.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.38 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.84 Å
Translation2.5 Å42.84 Å

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMAC5.8.0023refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UTQ

3utq


Resolution: 1.463→42.84 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1725 / WRfactor Rwork: 0.1444 / FOM work R set: 0.8863 / SU B: 2.415 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0588 / SU Rfree: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1808 3913 5 %RANDOM
Rwork0.1522 ---
obs0.1536 73875 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.6 Å2 / Biso mean: 18.305 Å2 / Biso min: 7.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.17 Å2
2---0.5 Å20 Å2
3---0.53 Å2
Refinement stepCycle: final / Resolution: 1.463→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3177 0 118 457 3752
Biso mean--35.98 31.33 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193540
X-RAY DIFFRACTIONr_bond_other_d0.0020.023203
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.944789
X-RAY DIFFRACTIONr_angle_other_deg0.91537374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8785420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53823.102187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96615565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0031533
X-RAY DIFFRACTIONr_chiral_restr0.120.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024039
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02884
X-RAY DIFFRACTIONr_mcbond_it1.1170.8911637
X-RAY DIFFRACTIONr_mcbond_other1.0690.8881634
X-RAY DIFFRACTIONr_mcangle_it1.7381.3252070
LS refinement shellResolution: 1.463→1.501 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 283 -
Rwork0.241 5477 -
all-5760 -
obs--99.95 %
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)
10.72820.25560.0451.80690.50120.66170.0566-0.05180.02920.1254-0.05680.10880.0387-0.04590.00020.0109-0.00670.0080.0065-0.00250.00850.1967-8.296127.6148
20.123-0.17870.34631.1493-1.90454.92660.03030.0590.0333-0.05040.00610.0249-0.1551-0.0554-0.03640.04280.0250.00850.04920.01080.037111.492718.04025.4642
33.04381.9771-0.22933.5051-0.05780.7891-0.14010.0998-0.2442-0.27950.141-0.40080.08230.1035-0.00090.04010.00780.03540.0281-0.01540.051422.0792-1.511712.3945
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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