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- PDB-5eu5: HLA Class I antigen -

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Basic information

Entry
Database: PDB / ID: 5eu5
TitleHLA Class I antigen
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Peptide antigen YLEPAPVTA
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 / melanosome membrane / melanosome organization / multivesicular body, internal vesicle / 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 / melanosome membrane / melanosome organization / multivesicular body, internal vesicle / multivesicular body membrane / 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 / Regulation of MITF-M-dependent genes involved in pigmentation / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / melanosome / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane
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 / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / MHC class I, alpha chain, C-terminal ...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 / 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
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: 1.54 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 1.4Nov 6, 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: Peptide antigen YLEPAPVTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,59739
Polymers44,7913
Non-polymers2,80736
Water3,711206
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-76 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.330, 79.640, 57.740
Angle α, β, γ (deg.)90.000, 116.220, 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


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 Peptide antigen YLEPAPVTA


Mass: 960.080 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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Non-polymers , 4 types, 242 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.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 0.2 M Ammonium Sulphate, 25 % PEG 4000
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.54→43.42 Å / Num. obs: 67308 / % possible obs: 99.6 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.042 / Net I/σ(I): 13 / Num. measured all: 244577
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.54-1.583.60.5822.31774549620.7580.35499.9
6.89-43.423.80.0335.929587870.9980.01798.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.54 Å43.42 Å
Translation1.54 Å43.42 Å

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Processing

Software
NameVersionClassification
Aimless0.2.12data scaling
PHASER2.5.5phasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I4W

4i4w


Resolution: 1.54→43.42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1946 / WRfactor Rwork: 0.1636 / FOM work R set: 0.8598 / SU B: 3.13 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0724 / SU Rfree: 0.0751 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2006 3406 5.1 %RANDOM
Rwork0.17 ---
obs0.1715 63875 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.81 Å2 / Biso mean: 19.751 Å2 / Biso min: 8.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.61 Å2
2---0.42 Å20 Å2
3---0.72 Å2
Refinement stepCycle: final / Resolution: 1.54→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 172 206 3537
Biso mean--37.29 30.08 -
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193501
X-RAY DIFFRACTIONr_bond_other_d0.0020.023183
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.9544719
X-RAY DIFFRACTIONr_angle_other_deg1.0837320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6095405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46823180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19915549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3251531
X-RAY DIFFRACTIONr_chiral_restr0.1210.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213881
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02854
X-RAY DIFFRACTIONr_mcbond_it0.8951.0071590
X-RAY DIFFRACTIONr_mcbond_other0.8951.0071589
X-RAY DIFFRACTIONr_mcangle_it1.5031.5031999
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 242 -
Rwork0.246 4715 -
all-4957 -
obs--99.88 %
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)
11.0280.1505-0.02161.81530.45810.93480.0327-0.04470.08830.1354-0.01440.13770.0381-0.0598-0.01830.0106-0.00240.01160.0062-0.00090.019156.0808-9.947627.5832
20.2931-0.1040.12481.0121-1.6845.34180.05360.09030.0534-0.0403-0.01820.0175-0.1877-0.084-0.03540.03790.02020.00790.04650.01020.020867.654416.53115.882
33.70592.44130.02313.70660.461.1513-0.14480.1542-0.3115-0.30090.1982-0.46410.03330.167-0.05330.0331-0.00030.03760.0432-0.02480.058278.226-2.814712.9519
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

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