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Yorodumi- PDB-4egc: Crystal Structure of MBP-fused Human Six1 Bound to Human Eya2 Eya... -
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-Basic information
Entry | Database: PDB / ID: 4egc | |||||||||
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Title | Crystal Structure of MBP-fused Human Six1 Bound to Human Eya2 Eya Domain | |||||||||
Components |
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Keywords | TRANSCRIPTION/HYDROLASE / homeodomain (HD) / six domain (SD) / eya domain (ED) / haloacid dehalogenase (HAD) / transcription factor / co-activator / protein phosphatase / DNA binding / fusion protein / nucleus / TRANSCRIPTION-HYDROLASE complex | |||||||||
Function / homology | Function and homology information regulation of skeletal muscle cell proliferation / mesonephric tubule formation / cellular response to 3,3',5-triiodo-L-thyronine / ureter smooth muscle cell differentiation / regulation of branch elongation involved in ureteric bud branching / positive regulation of secondary heart field cardioblast proliferation / olfactory placode formation / histone H2AXY142 phosphatase activity / myotome development / fungiform papilla morphogenesis ...regulation of skeletal muscle cell proliferation / mesonephric tubule formation / cellular response to 3,3',5-triiodo-L-thyronine / ureter smooth muscle cell differentiation / regulation of branch elongation involved in ureteric bud branching / positive regulation of secondary heart field cardioblast proliferation / olfactory placode formation / histone H2AXY142 phosphatase activity / myotome development / fungiform papilla morphogenesis / mesodermal cell fate specification / positive regulation of ureteric bud formation / regulation of skeletal muscle cell differentiation / facial nerve morphogenesis / otic vesicle development / regulation of synaptic assembly at neuromuscular junction / positive regulation of mesenchymal cell proliferation involved in ureter development / striated muscle tissue development / mitochondrial outer membrane permeabilization / trigeminal ganglion development / cochlea morphogenesis / metanephric mesenchyme development / neuron fate specification / myoblast migration / regulation of skeletal muscle satellite cell proliferation / aorta morphogenesis / embryonic skeletal system morphogenesis / positive regulation of branching involved in ureteric bud morphogenesis / chromatin => GO:0000785 / pattern specification process / pharyngeal system development / organ induction / anatomical structure development / embryonic cranial skeleton morphogenesis / regulation of epithelial cell proliferation / middle ear morphogenesis / ureteric bud development / regulation of neuron differentiation / inner ear morphogenesis / generation of neurons / branching involved in ureteric bud morphogenesis / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / outflow tract morphogenesis / inner ear development / thyroid gland development / carbohydrate transmembrane transporter activity / protein localization to nucleus / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / skeletal muscle fiber development / skeletal muscle tissue development / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of DNA repair / epithelial cell differentiation / positive regulation of brown fat cell differentiation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / protein-tyrosine-phosphatase / thymus development / kidney development / protein tyrosine phosphatase activity / sensory perception of sound / transcription coactivator binding / regulation of protein localization / sequence-specific double-stranded DNA binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / outer membrane-bounded periplasmic space / DNA-binding transcription activator activity, RNA polymerase II-specific / negative regulation of neuron apoptotic process / transcription regulator complex / sequence-specific DNA binding / cell differentiation / periplasmic space / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.994 Å | |||||||||
Authors | Zhao, R. / Patrick, A.N. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: Structure-function analyses of the human SIX1-EYA2 complex reveal insights into metastasis and BOR syndrome. Authors: Patrick, A.N. / Cabrera, J.H. / Smith, A.L. / Chen, X.S. / Ford, H.L. / Zhao, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4egc.cif.gz | 192.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4egc.ent.gz | 147.8 KB | Display | PDB format |
PDBx/mmJSON format | 4egc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/4egc ftp://data.pdbj.org/pub/pdb/validation_reports/eg/4egc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 62502.996 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: E172A,N173A,E359A,K362A,D363A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Gene: b4034, JW3994, malE, MBP, SIX1 / Plasmid: PMALX_B / Production host: Escherichia coli (E. coli) / Strain (production host): XA-90 / References: UniProt: P0AEX9, UniProt: Q15475 |
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#2: Protein | Mass: 33026.348 Da / Num. of mol.: 1 / Fragment: Eya domain (UNP residues 253-538) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EAB1, EYA2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA-90 / References: UniProt: O00167, protein-tyrosine-phosphatase |
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Sequence details | CHAIN A IS A CHIMERA (MBP FUSION) COMPRISING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 13.75% PEG8000, 0.01 M magnesium chloride, 0.05 M MES, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 85 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.48→50 Å / Num. obs: 145786 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.081 / Χ2: 0.841 / Net I/σ(I): 4.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.994→36.032 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.077 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.35 Å2 / Biso mean: 30.673 Å2 / Biso min: 13.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.994→36.032 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25
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