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- PDB-5eu6: HLA Class I antigen -

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Basic information

Entry
Database: PDB / ID: 5eu6
TitleHLA Class I antigen
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Human TCR Heavy Chain
  • Human TCR Light Chain
  • TYR-LEU-GLU-PRO-GLY-PRO-VAL-THR-VAL
KeywordsIMMUNE SYSTEM / IMMUNO / HLA-A02 / 1E6-TCR / Cross-reactivity
Function / homology
Function and homology information


cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / multivesicular body, internal vesicle / melanosome membrane / melanosome organization / multivesicular body membrane / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding ...cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / multivesicular body, internal vesicle / melanosome membrane / melanosome organization / multivesicular body membrane / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / T cell receptor complex / 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 / Regulation of MITF-M-dependent genes involved in pigmentation / beta-2-microglobulin binding / immune system process / 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 / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / 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 activation / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / MHC class II protein complex binding / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / antibacterial humoral response / tertiary granule lumen / melanosome / DAP12 signaling / positive regulation of protein binding / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / iron ion transport / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen
Similarity search - Function
PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / : / : / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain ...PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / : / : / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
T cell receptor alpha variable 21 / V_segment translation product / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Melanocyte protein PMEL / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsRizkallah, P.J. / Bianchi, V. / Cole, D.K. / Sewell, A.K.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A Molecular Switch Abrogates Glycoprotein 100 (gp100) T-cell Receptor (TCR) Targeting of a Human Melanoma Antigen.
Authors: Bianchi, V. / Bulek, A. / Fuller, A. / Lloyd, A. / Attaf, M. / Rizkallah, P.J. / Dolton, G. / Sewell, A.K. / Cole, D.K.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2May 11, 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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 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: TYR-LEU-GLU-PRO-GLY-PRO-VAL-THR-VAL
D: Human TCR Light Chain
E: Human TCR Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,85526
Polymers94,1895
Non-polymers1,66521
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14830 Å2
ΔGint-147 kcal/mol
Surface area38480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.520, 54.410, 112.120
Angle α, β, γ (deg.)85.010, 81.640, 72.630
Int Tables number1
Space group name H-MP1

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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


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 TYR-LEU-GLU-PRO-GLY-PRO-VAL-THR-VAL


Mass: 974.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) / References: UniProt: P40967*PLUS

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Antibody , 2 types, 2 molecules DE

#4: Antibody Human TCR Light Chain


Mass: 22238.629 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) / References: UniProt: A0A0B4J279*PLUS
#5: Antibody Human TCR Heavy Chain


Mass: 27146.068 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) / References: UniProt: A0A592*PLUS

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Non-polymers , 4 types, 254 molecules

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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium sulphate, 0.1 M Bis Tris propane pH 6.5, 20% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.02→51.873 Å / Num. all: 64983 / Num. obs: 64983 / % possible obs: 97.7 % / Redundancy: 2 % / Rpim(I) all: 0.057 / Rrim(I) all: 0.087 / Rsym value: 0.078 / Net I/av σ(I): 5.688 / Net I/σ(I): 5.5 / Num. measured all: 128191
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
2.02-2.071.90.3961.6895547850.3980.3961.996.7
2.07-2.1320.2912.2907645910.3090.2912.396.1
2.13-2.191.90.2842.2868845330.2880.2842.696.9
2.19-2.2620.2292.8872743990.2340.2293.297.1
2.26-2.3320.1773.7864042510.1830.1773.797.1
2.33-2.4120.1663.8826141180.1650.166497.4
2.41-2.5120.1324.8808539960.1340.1324.697.4
2.51-2.611.90.125.8748538830.1130.125.197.8
2.61-2.721.90.1036.4721737030.0930.1035.897.7
2.72-2.861.90.0966.6688135660.0830.0966.598.3
2.86-3.0120.0866.8686533820.0720.0867.298.5
3.01-3.1920.087.8651531870.0620.08898.5
3.19-3.4120.0748.3607529890.0540.0748.598.2
3.41-3.691.90.0767.9542727980.0510.0768.898.3
3.69-4.041.90.079.8499325930.0490.07998.7
4.04-4.521.90.06310.1455323490.0430.0639.298.9
4.52-5.222.10.05512.2422520430.040.0559.698.7
5.22-6.3920.05711.3343617390.0370.0579.498.5
6.39-9.031.90.05312.5259613680.0380.0539.299.1
9.03-51.8732.10.05212.814917100.0320.0529.997.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I4W

4i4w


Resolution: 2.02→51.87 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2486 / WRfactor Rwork: 0.2001 / FOM work R set: 0.8419 / SU B: 9.093 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1706 / SU Rfree: 0.1548 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 3294 5.1 %RANDOM
Rwork0.1811 ---
obs0.1832 61688 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 166.79 Å2 / Biso mean: 55.445 Å2 / Biso min: 20.24 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20.72 Å20.86 Å2
2---1.48 Å20.72 Å2
3---0.76 Å2
Refinement stepCycle: final / Resolution: 2.02→51.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 98 233 6967
Biso mean--65.31 44.83 -
Num. residues----833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196907
X-RAY DIFFRACTIONr_bond_other_d0.0020.026233
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.9439367
X-RAY DIFFRACTIONr_angle_other_deg1.164314359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0425832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54723.889342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.936151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8061548
X-RAY DIFFRACTIONr_chiral_restr0.160.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217843
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021657
X-RAY DIFFRACTIONr_mcbond_it1.1842.3163337
X-RAY DIFFRACTIONr_mcbond_other1.1842.3163336
X-RAY DIFFRACTIONr_mcangle_it1.833.4634166
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 243 -
Rwork0.262 4533 -
all-4776 -
obs--96.74 %
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)
11.72060.02630.38382.4920.20472.10430.12080.0703-0.0875-0.2807-0.06970.04560.04720.0735-0.0510.04370.0123-0.02510.00870.00540.079718.860248.3826-35.8508
25.67361.3721-1.77986.1919-1.69865.9210.07210.73770.5261-0.69440.0383-0.4477-0.47820.6999-0.11050.43290.0490.00440.49350.03240.184420.411766.155-67.1188
33.6942-1.09121.59813.0292-1.08794.29260.07880.23720.2171-0.1559-0.07120.326-0.5231-0.2868-0.00770.20250.06290.0040.09550.01790.16837.689569.8019-48.4379
42.474-1.8580.32995.0786-1.56322.7881-0.0616-0.1184-0.0488-0.06170.0559-0.17670.14140.22590.00570.0352-0.0081-0.02420.066-0.00370.09924.442820.6479-19.8933
53.60430.1524-3.09630.8321-1.41245.29230.026-0.189-0.5464-0.0241-0.05020.49970.74440.14370.02421.14880.14510.15850.82950.08880.916919.21961.397111.2118
62.4090.5831-1.62472.6212-1.20624.2240.0454-0.24570.06190.3780.0270.3175-0.1734-0.2914-0.07240.07690.00280.00890.09890.00010.126211.223237.2446-9.8277
75.8577-2.05561.97963.0778-0.90293.8448-0.1807-0.4435-0.2880.39490.18530.15240.3080.3028-0.00460.54570.00710.12440.57690.14110.22916.424918.518414.193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 115
6X-RAY DIFFRACTION5D116 - 204
7X-RAY DIFFRACTION6E2 - 115
8X-RAY DIFFRACTION7E116 - 245

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