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- PDB-3myj: Human Class I MHC HLA-A2 in complex with the WT-1 (126-134) (R1Y)... -

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Basic information

Entry
Database: PDB / ID: 3myj
TitleHuman Class I MHC HLA-A2 in complex with the WT-1 (126-134) (R1Y) peptide variant.
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Wilms tumor protein
KeywordsIMMUNE SYSTEM / WT-1 peptide / R1Y mutation / nonapeptide / MHC class I / HLA-A2 / cancer vaccine / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


posterior mesonephric tubule development / negative regulation of metanephric glomerular mesangial cell proliferation / positive regulation of metanephric ureteric bud development / thorax and anterior abdomen determination / metanephric epithelium development / regulation of animal organ formation / adrenal cortex formation / negative regulation of female gonad development / positive regulation of heart growth / visceral serous pericardium development ...posterior mesonephric tubule development / negative regulation of metanephric glomerular mesangial cell proliferation / positive regulation of metanephric ureteric bud development / thorax and anterior abdomen determination / metanephric epithelium development / regulation of animal organ formation / adrenal cortex formation / negative regulation of female gonad development / positive regulation of heart growth / visceral serous pericardium development / Nephron development / glomerular basement membrane development / diaphragm development / sex determination / positive regulation of male gonad development / cellular response to gonadotropin stimulus / gonad development / Transcriptional regulation of testis differentiation / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / podocyte differentiation / tissue development / double-stranded methylated DNA binding / cardiac muscle cell fate commitment / hemi-methylated DNA-binding / mesenchymal to epithelial transition / male genitalia development / glomerulus development / camera-type eye development / C2H2 zinc finger domain binding / ureteric bud development / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / adrenal gland development / positive regulation of CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / branching involved in ureteric bud morphogenesis / CD8 receptor binding / negative regulation of gene expression via chromosomal CpG island methylation / antigen processing and presentation of exogenous peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / endoplasmic reticulum exit site / germ cell development / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / vasculogenesis / T cell receptor binding / epithelial cell differentiation / RNA splicing / cellular response to cAMP / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / kidney development / cellular response to iron(III) ion / 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 / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / negative regulation of cell growth / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of miRNA transcription / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / male gonad development / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of type II interferon production / phagocytic vesicle membrane / positive regulation of immune response / recycling endosome membrane / Interferon gamma signaling
Similarity search - Function
Wilm's tumour protein, N-terminal / Wilm's tumour protein / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / MHC class I-like antigen recognition-like ...Wilm's tumour protein, N-terminal / Wilm's tumour protein / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Zinc finger C2H2-type / 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 / Wilms tumor protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsBorbulevych, O.Y. / Baker, B.M.
CitationJournal: Mol.Immunol. / Year: 2010
Title: Structures of native and affinity-enhanced WT1 epitopes bound to HLA-A*0201: Implications for WT1-based cancer therapeutics.
Authors: Borbulevych, O.Y. / Do, P. / Baker, B.M.
History
DepositionMay 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: Wilms tumor protein
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Wilms tumor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7907
Polymers89,6986
Non-polymers921
Water8,971498
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Wilms tumor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9414
Polymers44,8493
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-23 kcal/mol
Surface area18920 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Wilms tumor protein


Theoretical massNumber of molelcules
Total (without water)44,8493
Polymers44,8493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-22 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.202, 62.826, 74.755
Angle α, β, γ (deg.)81.910, 75.900, 77.940
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLUGLUAA182 - 275182 - 275
21THRTHRGLUGLUDD182 - 275182 - 275
12METMETMETMETBB0 - 991 - 100
22METMETMETMETEE0 - 991 - 100

NCS ensembles :
ID
1
2

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Components

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


Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: residue 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide Wilms tumor protein / WT33


Mass: 1115.300 Da / Num. of mol.: 2 / Fragment: residues 126-134 / Source method: obtained synthetically / Details: Peptide synthesis / Source: (synth.) homo sapiens (human) / References: UniProt: P19544
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350 24%, MES 0.025M, KCl 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorDetector: CCD
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.89→20 Å / Num. all: 68117 / Num. obs: 66006 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.232 / Net I/σ(I): 14.5
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2 / Num. unique all: 3304 / Χ2: 1.098 / % possible all: 95.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.6 Å19.81 Å
Translation3.6 Å19.81 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TVB

1tvb


Resolution: 1.89→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.836 / SU B: 8.365 / SU ML: 0.109 / SU R Cruickshank DPI: 0.161 / SU Rfree: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3333 5.1 %RANDOM, 5 %
Rwork0.185 ---
all0.188 68568 --
obs0.188 65990 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 51.1 Å2 / Biso mean: 20.664 Å2 / Biso min: 7.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.89 Å20.58 Å2
2---0.72 Å20.33 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.89→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6326 0 6 498 6830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0216599
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.9248976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7725786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52323.25360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.133151073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0241556
X-RAY DIFFRACTIONr_chiral_restr0.1390.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215234
X-RAY DIFFRACTIONr_mcbond_it1.061.53866
X-RAY DIFFRACTIONr_mcangle_it1.82826248
X-RAY DIFFRACTIONr_scbond_it3.01132733
X-RAY DIFFRACTIONr_scangle_it4.6674.52716
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A736MEDIUM POSITIONAL0.260.5
1A736MEDIUM THERMAL1.152
2B836MEDIUM POSITIONAL0.260.5
2B836MEDIUM THERMAL12
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 225 -
Rwork0.267 4148 -
all-4373 -
obs--87.02 %
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)
11.18940.17860.12721.4493-0.45832.2473-0.03530.02280.18410.0666-0.01790.0535-0.23050.00150.05330.06320.026-0.00330.0389-0.00910.04842.58713.6936.676
21.9158-2.0619-1.1784.42832.08843.27550.12050.155-0.0855-0.3601-0.0925-0.02520.22610.0651-0.02810.10310.0221-0.00610.0243-0.00930.02586.002-19.674-6.36
32.06391.8768-0.57073.9565-0.80811.737-0.07470.12270.0222-0.13280.11490.30480.0877-0.2307-0.04030.01970.0057-0.00430.08210.01590.0405-11.169-4.894-7.043
40.9396-0.24080.17861.76660.50041.9415-0.06710.00990.08730.05770.0449-0.1163-0.0830.09870.02220.0620.01950.01470.05210.02210.029429.546-13.52926.29
54.27791.4652-2.75772.2306-1.03012.84790.0840.0121-0.03970.0145-0.08410.0061-0.0267-0.15470.00010.02270.01220.0070.03730.00990.014412.836-42.57238.971
60.8801-0.63790.14374.88270.58892.24120.009-0.0291-0.06880.05540.013-0.15170.05010.0364-0.02210.01590.02520.00110.04760.00930.016634.417-36.22839.705
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 182
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A183 - 275
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 182
6X-RAY DIFFRACTION4F1 - 9
7X-RAY DIFFRACTION5D183 - 275
8X-RAY DIFFRACTION6E0 - 99

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