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- PDB-1b8i: STRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1b8i
TitleSTRUCTURE OF THE HOMEOTIC UBX/EXD/DNA TERNARY COMPLEX
Components
  • DNA (5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3')
  • DNA (5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3')
  • PROTEIN (HOMEOBOX PROTEIN EXTRADENTICLE)
  • PROTEIN (ULTRABITHORAX HOMEOTIC PROTEIN IV)
KeywordsTRANSCRIPTION/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 / eye development / regulation of cell fate specification / peripheral nervous system development / cell fate determination / anterior/posterior pattern specification / midgut development / transcription factor binding / neuron development / embryonic organ development / cis-regulatory region sequence-specific DNA binding / transcription repressor complex / transcription coregulator binding / protein-DNA complex / transcription coregulator activity / 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 / DNA-binding transcription factor activity / protein heterodimerization activity / protein domain specific binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive 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
PBX, PBC domain / PBC domain / PBC domain profile. / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox KN domain / Homeobox KN domain / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. ...PBX, PBC domain / PBC domain / PBC domain profile. / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox KN domain / Homeobox KN domain / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox protein extradenticle / Homeotic protein ultrabithorax
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.4 Å
AuthorsPassner, J.M. / Ryoo, H.-D. / Shen, L. / Mann, R.S. / Aggarwal, A.K.
CitationJournal: 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
DepositionFeb 1, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3')
D: DNA (5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3')
A: PROTEIN (ULTRABITHORAX HOMEOTIC PROTEIN IV)
B: PROTEIN (HOMEOBOX PROTEIN EXTRADENTICLE)


Theoretical massNumber of molelcules
Total (without water)26,7304
Polymers26,7304
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.430, 69.430, 100.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain DNA (5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*C)-3')


Mass: 4537.975 Da / Num. of mol.: 1 / Fragment: UBX/EXD CONSENSUS BINDING SITE / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*G)-3')


Mass: 4640.020 Da / Num. of mol.: 1 / Fragment: UBX/EXD CONSENSUS BINDING SITE / Source method: obtained synthetically
#3: Protein PROTEIN (ULTRABITHORAX HOMEOTIC PROTEIN IV) / ULTRABITHORAX


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: NUCLEUSCell 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 PROTEIN (HOMEOBOX PROTEIN EXTRADENTICLE) / PBX 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: NUCLEUSCell nucleus / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P40427
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 40 %
Crystal growMethod: 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

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.93
DetectorType: ADSC / Detector: CCD / Date: Dec 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
MLPHAREphasing
SHARPphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.304 508 5.4 %RANDOM
Rwork0.224 ---
obs-9490 96.7 %-
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1--8.3 Å20 Å20 Å2
2---8.3 Å20 Å2
3---16.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-8 Å
Luzzati sigma a0.28 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 609 0 110 1747
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.95
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.96
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it6.741.5
X-RAY DIFFRACTIONx_mcangle_it9.32
X-RAY DIFFRACTIONx_scbond_it7.222
X-RAY DIFFRACTIONx_scangle_it9.892.5
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.057 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.324 50 4.5 %
Rwork0.32 1052 -
obs--92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3TOPH19.SOL
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
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.96
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.324 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.32

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