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- PDB-4wuu: Structure of ESK1 in complex with HLA-A*0201/WT1 -

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Basic information

Entry
Database: PDB / ID: 4wuu
TitleStructure of ESK1 in complex with HLA-A*0201/WT1
Components
  • ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU
  • Beta-2-microglobulin
  • ESK1
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • IMMUNOGLOBULIN HEAVY CHAIN
KeywordsIMMUNE SYSTEM / antibody / MHC 1 / WT1 / HLA-A*0201
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 / mesenchymal to epithelial transition / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / positive regulation of male gonad development / cellular response to gonadotropin stimulus / Transcriptional regulation of testis differentiation / gonad development / podocyte differentiation / cardiac muscle cell fate commitment / double-stranded methylated DNA binding / hemi-methylated DNA-binding / tissue development / male genitalia development / glomerulus development / camera-type eye development / C2H2 zinc finger domain binding / ureteric bud development / negative regulation of gene expression via chromosomal CpG island methylation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / branching involved in ureteric bud morphogenesis / adrenal gland development / 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 / germ cell development / 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 / vasculogenesis / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / cellular response to cAMP / epithelial cell differentiation / RNA splicing / 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 / kidney development / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / negative regulation of cell growth / 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 miRNA transcription / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / male gonad development
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. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / 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 / 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 / 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 / Wilms tumor protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.047 Å
AuthorsAtaie, N.J. / Ng, H.L.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structure of a TCR-Mimic Antibody with Target Predicts Pharmacogenetics.
Authors: Ataie, N. / Xiang, J. / Cheng, N. / Brea, E.J. / Lu, W. / Scheinberg, D.A. / Liu, C. / Ng, H.L.
History
DepositionNov 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU
D: ESK1
E: IMMUNOGLOBULIN HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)93,9425
Polymers93,9425
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.080, 118.260, 126.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34081.648 Da / Num. of mol.: 1 / Fragment: UNP 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: UNP 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
#3: Protein/peptide ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU


Mass: 1109.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P19544*PLUS
#4: Antibody ESK1


Mass: 22750.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#5: Antibody IMMUNOGLOBULIN HEAVY CHAIN


Mass: 24121.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.25 / Details: 0.1 M Bis-Tris HCl pH 5.5, 25 percent PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.047→33.44 Å / Num. obs: 21106 / % possible obs: 97.6 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 12.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.047→33.44 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 17.28 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2002 9.77 %RANDOM
Rwork0.1984 ---
obs0.204 20499 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.047→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6422 0 0 0 6422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046609
X-RAY DIFFRACTIONf_angle_d0.7429002
X-RAY DIFFRACTIONf_dihedral_angle_d15.0593907
X-RAY DIFFRACTIONf_chiral_restr0.045952
X-RAY DIFFRACTIONf_plane_restr0.0051164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0472-3.12340.40851320.31711185X-RAY DIFFRACTION92
3.1234-3.20770.35471360.26821315X-RAY DIFFRACTION99
3.2077-3.30210.31361510.25891274X-RAY DIFFRACTION100
3.3021-3.40850.34631260.26671327X-RAY DIFFRACTION100
3.4085-3.53020.33271510.25721332X-RAY DIFFRACTION100
3.5302-3.67140.32591320.231304X-RAY DIFFRACTION100
3.6714-3.83830.27311500.21171319X-RAY DIFFRACTION100
3.8383-4.04030.27471450.20711305X-RAY DIFFRACTION100
4.0403-4.2930.21931400.17981323X-RAY DIFFRACTION100
4.293-4.62360.23721400.16331332X-RAY DIFFRACTION100
4.6236-5.08750.21691420.15611350X-RAY DIFFRACTION100
5.0875-5.82030.21591500.17061337X-RAY DIFFRACTION100
5.8203-7.32030.26961500.19961356X-RAY DIFFRACTION100
7.3203-33.44180.19291570.1761438X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.017 Å / Origin y: -28.5512 Å / Origin z: 45.4187 Å
111213212223313233
T0.3273 Å20.022 Å20.0328 Å2-0.3935 Å20.0044 Å2--0.3777 Å2
L0.1286 °20.0913 °2-0.0318 °2-1.3274 °2-0.9678 °2--0.9196 °2
S-0.0784 Å °0.0172 Å °-0.0593 Å °-0.1099 Å °0.005 Å °-0.1097 Å °0.1052 Å °-0.0679 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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