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- PDB-6eqb: HLA class I histocompatibility antigen -

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Basic information

Entry
Database: PDB / ID: 6eqb
TitleHLA class I histocompatibility antigen
Components
  • (High Affinity Mel5 TCR, ...) x 2
  • ALA-ALA-GLY-ILE-GLY-ILE-LEU-THR-VAL
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / Melanoma / vaccine / TCR / MHC / 3D Structure
Function / homology
Function and homology information


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 memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 ...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 memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / endoplasmic reticulum exit site / beta-2-microglobulin binding / 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 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 / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / 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 / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / positive regulation of protein binding / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / antibacterial humoral response / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / 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 classes I/II-like antigen recognition protein ...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
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: 2.81 Å
AuthorsRizkallah, P.J. / Cole, D.K.
CitationJournal: Eur.J.Immunol. / Year: 2019
Title: TCR-induced alteration of primary MHC peptide anchor residue.
Authors: Madura, F. / Rizkallah, P.J. / Legut, M. / Holland, C.J. / Fuller, A. / Bulek, A. / Schauenburg, A.J. / Trimby, A. / Hopkins, J.R. / Wells, S.A. / Godkin, A. / Miles, J.J. / Sami, M. / Li, Y. ...Authors: Madura, F. / Rizkallah, P.J. / Legut, M. / Holland, C.J. / Fuller, A. / Bulek, A. / Schauenburg, A.J. / Trimby, A. / Hopkins, J.R. / Wells, S.A. / Godkin, A. / Miles, J.J. / Sami, M. / Li, Y. / Liddy, N. / Jakobsen, B.K. / Loveridge, E.J. / Cole, D.K. / Sewell, A.K.
History
DepositionOct 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Structure summary / Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: ALA-ALA-GLY-ILE-GLY-ILE-LEU-THR-VAL
D: High Affinity Mel5 TCR, alpha chain
E: High Affinity Mel5 TCR, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,76113
Polymers93,7765
Non-polymers9858
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13040 Å2
ΔGint-101 kcal/mol
Surface area38400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.771, 120.771, 82.247
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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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


Mass: 31951.316 Da / Num. of mol.: 1
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
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 ALA-ALA-GLY-ILE-GLY-ILE-LEU-THR-VAL


Mass: 813.982 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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High Affinity Mel5 TCR, ... , 2 types, 2 molecules DE

#4: Protein High Affinity Mel5 TCR, alpha chain


Mass: 21739.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein High Affinity Mel5 TCR, beta chain


Mass: 27391.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 26 molecules

#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 20% PEG 4000 and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.808→120.771 Å / Num. all: 29094 / Num. obs: 29094 / % possible obs: 100 % / Redundancy: 8 % / Rpim(I) all: 0.058 / Rrim(I) all: 0.165 / Rsym value: 0.146 / Net I/av σ(I): 4.6 / Net I/σ(I): 9.9 / Num. measured all: 233037
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.81-2.888.21.1560.721220.4641.3281.156100
2.88-2.968.20.9610.820740.3841.0990.961100
2.96-3.058.20.737120470.2950.8440.737100
3.05-3.148.10.5581.419440.2230.6370.558100
3.14-3.248.10.4441.719220.1770.5070.444100
3.24-3.368.10.3232.418460.1280.3670.323100
3.36-3.488.10.2642.917880.1050.3010.264100
3.48-3.628.10.2123.617120.0840.240.212100
3.62-3.798.10.1664.516630.0660.1870.166100
3.79-3.978.10.1365.415700.0540.1540.136100
3.97-4.1980.116.514930.0430.1230.11100
4.19-4.4480.0897.514330.0350.10.089100
4.44-4.757.90.0887.513510.0340.0980.088100
4.75-5.137.90.0986.512360.0380.1090.098100
5.13-5.627.70.1145.511650.0450.1260.114100
5.62-6.287.50.1324.810430.0520.1450.132100
6.28-7.256.90.0996.39260.0410.110.099100
7.25-8.888.20.05112.57810.0190.0560.051100
8.88-12.568.10.049126210.0180.0530.049100
12.56-120.7717.40.0512.13570.0230.060.0598.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.29 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.81 Å120.77 Å
Translation2.81 Å120.77 Å

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HG1

3hg1


Resolution: 2.81→120.77 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.886 / SU B: 32.363 / SU ML: 0.288 / SU R Cruickshank DPI: 1.7653 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.765 / ESU R Free: 0.355
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 1478 5.1 %RANDOM
Rwork0.1831 ---
obs0.1865 27589 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 206.49 Å2 / Biso mean: 76.052 Å2 / Biso min: 25.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å2-0 Å2-0 Å2
2--0.98 Å2-0 Å2
3----1.95 Å2
Refinement stepCycle: final / Resolution: 2.81→120.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6609 0 58 18 6685
Biso mean--111 55.88 -
Num. residues----825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0196915
X-RAY DIFFRACTIONr_bond_other_d0.0020.026223
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.9369397
X-RAY DIFFRACTIONr_angle_other_deg1.168314339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.515832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44423.868349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.013151095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2121548
X-RAY DIFFRACTIONr_chiral_restr0.1240.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217896
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021692
LS refinement shellResolution: 2.808→2.881 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 122 -
Rwork0.353 1999 -
all-2121 -
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)
13.58980.0775-1.34973.4646-0.68033.4566-0.07320.1268-0.225-0.0209-0.0235-0.2940.26430.34070.09670.08810.00680.02780.3189-0.04080.050754.6115-7.50926.5385
26.638-3.49380.13533.09591.23781.5491-0.2343-0.0537-0.37770.17890.6309-0.51150.27310.9698-0.39661.05360.18440.24281.03540.31411.208878.1497-34.422121.4823
33.90141.3948-0.44766.7610.86033.8225-0.11860.4286-0.9537-0.7859-0.174-0.00321.082-0.30960.29260.57250.0050.08250.5542-0.05620.380763.5519-23.74586.6244
44.5823-0.8976-1.80441.71520.64533.1481-0.0973-0.49370.1810.28790.141-0.1020.08140.2893-0.04370.1398-0.0442-0.0260.2915-0.01450.011935.44012.602147.5929
58.6561-0.0022.55446.23710.16375.96860.068-0.74050.01280.20730.04990.4148-0.1323-0.6501-0.11790.62810.0810.02450.6193-0.05770.24826.987719.593758.5186
68.5059-1.95920.2571.71060.10211.62590.20510.5090.1808-0.299-0.06290.1914-0.19150.0731-0.14230.26890.0238-0.01370.22630.03420.068729.22716.076325.5981
73.69820.45091.33412.62432.28767.3327-0.0896-0.40040.1090.2190.0145-0.2569-0.3373-0.0140.07510.34740.0392-0.09710.24010.09780.17139.304223.249542.3514
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
5X-RAY DIFFRACTION4D3 - 110
6X-RAY DIFFRACTION5D115 - 200
7X-RAY DIFFRACTION6E1 - 110
8X-RAY DIFFRACTION7E115 - 241

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