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- PDB-5zjs: Structure of AbdB/Exd complex bound to a 'Blue14' DNA sequence -

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Basic information

Entry
Database: PDB / ID: 5zjs
TitleStructure of AbdB/Exd complex bound to a 'Blue14' DNA sequence
Components
  • DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*TP*AP*AP*TP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*AP*TP*TP*AP*AP*TP*CP*AP*TP*GP*C)-3')
  • Homeobox protein abdominal-B
  • Homeobox protein extradenticle
KeywordsTRANSCRIPTION/DNA / AbdB / Exd / DNA / shape / specificity / Hox / Homeodomain / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


genital disc sexually dimorphic development / male pigmentation / negative regulation of cardioblast cell fate specification / sperm storage / negative regulation of salivary gland boundary specification / specification of segmental identity, abdomen / imaginal disc-derived female genitalia development / determination of genital disc primordium / external genitalia morphogenesis / salivary gland boundary specification ...genital disc sexually dimorphic development / male pigmentation / negative regulation of cardioblast cell fate specification / sperm storage / negative regulation of salivary gland boundary specification / specification of segmental identity, abdomen / imaginal disc-derived female genitalia development / determination of genital disc primordium / external genitalia morphogenesis / salivary gland boundary specification / oenocyte development / gonadal mesoderm development / female genitalia development / somatic muscle development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / open tracheal system development / negative regulation of female receptivity / polytene chromosome band / neuroendocrine cell differentiation / positive regulation of apoptotic process involved in morphogenesis / negative regulation of striated muscle tissue development / segment specification / midgut development / eye development / regulation of cell fate specification / male genitalia development / peripheral nervous system development / germ cell migration / embryonic organ development / neuron development / cis-regulatory region sequence-specific DNA binding / animal organ morphogenesis / transcription coregulator activity / protein-DNA complex / brain development / RNA polymerase II transcription regulator complex / male gonad development / transcription regulator complex / DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Homeobox protein Hox-A10/abdominal-B-like / PBX, PBC domain / PBC domain / PBC domain profile. / : / Homeobox KN domain / Homeobox KN domain / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. ...Homeobox protein Hox-A10/abdominal-B-like / PBX, PBC domain / PBC domain / PBC domain profile. / : / 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 abdominal-B / Homeobox protein extradenticle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.896 Å
AuthorsBaburajendran, N. / Zeiske, T. / Kaczynska, A. / Mann, R. / Honig, B. / Shapiro, L. / Palmer, A.G.
CitationJournal: Cell Rep / Year: 2018
Title: Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.
Authors: Zeiske, T. / Baburajendran, N. / Kaczynska, A. / Brasch, J. / Palmer, A.G. / Shapiro, L. / Honig, B. / Mann, R.S.
History
DepositionMar 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homeobox protein abdominal-B
B: Homeobox protein extradenticle
C: DNA (5'-D(*GP*TP*CP*AP*TP*TP*AP*AP*TP*CP*AP*TP*GP*C)-3')
D: DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*TP*AP*AP*TP*GP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,5284
Polymers27,5284
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-24 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.760, 49.658, 96.774
Angle α, β, γ (deg.)90.000, 109.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Homeobox protein abdominal-B / Infraabdominal 7 / IAB-7 / P3 / PH189


Mass: 10195.751 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Abd-B, CG10291 / Production host: Escherichia coli (E. coli) / References: UniProt: P09087
#2: Protein Homeobox protein extradenticle / Dpbx


Mass: 8773.827 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: exd, CG8933 / Production host: Escherichia coli (E. coli) / References: UniProt: P40427
#3: DNA chain DNA (5'-D(*GP*TP*CP*AP*TP*TP*AP*AP*TP*CP*AP*TP*GP*C)-3')


Mass: 4254.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#4: DNA chain DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*TP*AP*AP*TP*GP*AP*C)-3')


Mass: 4303.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200mM MgCl2, 0.1M Tris pH 5.8, 17.5% PEG 3350, 2.5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.896→28.143 Å / Num. obs: 7524 / % possible obs: 94.74 % / Redundancy: 1.9 % / Biso Wilson estimate: 41.58 Å2 / Net I/σ(I): 9.16
Reflection shellResolution: 2.896→2.999 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZJQ

5zjq


Resolution: 2.896→28.143 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2813 343 4.61 %
Rwork0.2532 7093 -
obs0.2546 7436 93.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.3 Å2 / Biso mean: 62.7866 Å2 / Biso min: 25.65 Å2
Refinement stepCycle: final / Resolution: 2.896→28.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 568 0 3 1586
Biso mean---30 -
Num. residues----158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041673
X-RAY DIFFRACTIONf_angle_d0.6972380
X-RAY DIFFRACTIONf_chiral_restr0.029257
X-RAY DIFFRACTIONf_plane_restr0.002210
X-RAY DIFFRACTIONf_dihedral_angle_d25.139633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8957-3.64710.30991630.2693451361492
3.6471-28.14470.26921800.2463642382295
Refinement TLS params.Method: refined / Origin x: -17.9431 Å / Origin y: 2.2398 Å / Origin z: 122.0441 Å
111213212223313233
T0.3138 Å2-0.0756 Å20.0036 Å2-0.3293 Å2-0.0194 Å2--0.3727 Å2
L1.403 °2-0.1435 °2-0.7476 °2-0.674 °2-0.2397 °2--1.3968 °2
S-0.1831 Å °0.3474 Å °0.1425 Å °-0.2013 Å °0.1786 Å °0.0386 Å °0.1249 Å °0.2114 Å °0.0366 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA13 - 77
2X-RAY DIFFRACTION1allB3 - 74
3X-RAY DIFFRACTION1allC1 - 14
4X-RAY DIFFRACTION1allD1 - 14
5X-RAY DIFFRACTION1allE1 - 3

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