+Open data
-Basic information
Entry | Database: PDB / ID: 1b8i | ||||||
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Title | STRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / DNA BINDING / HOMEODOMAIN / HOMEOTIC PROTEINS / DEVELOPMENT / SPECIFICITY / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information dorsal vessel aortic cell fate commitment / positive regulation of muscle organ development / anterior Malpighian tubule development / specification of animal organ identity / regulation of imaginal disc growth / salivary gland boundary specification / haltere development / oenocyte development / mesodermal cell fate specification / specification of segmental identity, thorax ...dorsal vessel aortic cell fate commitment / positive regulation of muscle organ development / anterior Malpighian tubule development / specification of animal organ identity / regulation of imaginal disc growth / salivary gland boundary specification / haltere development / oenocyte development / mesodermal cell fate specification / specification of segmental identity, thorax / open tracheal system development / imaginal disc-derived leg morphogenesis / somatic muscle development / muscle cell fate specification / polytene chromosome band / endoderm formation / midgut development / eye development / regulation of cell fate specification / peripheral nervous system development / cell fate determination / anterior/posterior pattern specification / neuron development / cis-regulatory region sequence-specific DNA binding / embryonic organ development / transcription coregulator activity / transcription coregulator binding / transcription repressor complex / protein-DNA complex / animal organ morphogenesis / brain development / RNA polymerase II transcription regulator complex / heart development / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / protein heterodimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.4 Å | ||||||
Authors | Passner, J.M. / Ryoo, H.-D. / Shen, L. / Mann, R.S. / Aggarwal, A.K. | ||||||
Citation | Journal: Nature / Year: 1999 Title: Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex. Authors: Passner, J.M. / Ryoo, H.D. / Shen, L. / Mann, R.S. / Aggarwal, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b8i.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b8i.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 1b8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b8i_validation.pdf.gz | 386.7 KB | Display | wwPDB validaton report |
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Full document | 1b8i_full_validation.pdf.gz | 398.1 KB | Display | |
Data in XML | 1b8i_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1b8i_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b8i ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b8i | HTTPS FTP |
-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
#1: DNA chain | Mass: 4537.975 Da / Num. of mol.: 1 / Fragment: UBX/EXD CONSENSUS BINDING SITE / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4640.020 Da / Num. of mol.: 1 / Fragment: UBX/EXD CONSENSUS BINDING SITE / Source method: obtained synthetically |
#3: Protein | Mass: 9998.532 Da / Num. of mol.: 1 / Fragment: YPWM MOTIF AND HOMEODOMAIN / Mutation: C139S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Description: IVA SPLICING ISOFORM OF THE UBX GENE WAS USED; / Cellular location: NUCLEUS / Gene: UBX / Plasmid: PET-3A / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P83949 |
#4: Protein | Mass: 7553.561 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cellular location: NUCLEUS / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P40427 |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 40 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.6M AMMONIUM PHOSPHATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP |
Crystal grow | *PLUS Method: unknown |
Components of the solutions | *PLUS Conc.: 0.6 M / Common name: ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.93 |
Detector | Type: ADSC / Detector: CCD / Date: Dec 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 10324 / % possible obs: 98.3 % / Redundancy: 10.5 % / Biso Wilson estimate: 48.2 Å2 / Rsym value: 7.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Rsym value: 18.5 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 110271 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.185 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.4→8 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 42.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Rfactor Rfree error: 0.057 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5.4 % / Rfactor obs: 0.224 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 42.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.324 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.32 |