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- PDB-5zjq: Structure of AbdB/Exd complex bound to a 'Red14' DNA sequence -

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Basic information

Entry
Database: PDB / ID: 5zjq
TitleStructure of AbdB/Exd complex bound to a 'Red14' DNA sequence
Components
  • DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*TP*TP*AP*TP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*AP*TP*GP*C)-3')
  • Homeobox protein abdominal-B
  • Homeobox protein extradenticle
KeywordsTRANSCRIPTION/DNA / AbdB / Exd / DNA / shape / specificity / 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 / open tracheal system development / somatic muscle development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / negative regulation of female receptivity / polytene chromosome band / negative regulation of striated muscle tissue development / neuroendocrine cell differentiation / positive regulation of apoptotic process involved in morphogenesis / segment specification / eye development / regulation of cell fate specification / male genitalia development / peripheral nervous system development / germ cell migration / midgut development / embryonic organ development / cis-regulatory region sequence-specific DNA binding / neuron development / animal organ morphogenesis / transcription coregulator activity / protein-DNA complex / brain development / RNA polymerase II transcription regulator complex / male gonad 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 / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor 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: 2.443 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*AP*AP*AP*TP*CP*AP*TP*GP*C)-3')
D: DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*TP*TP*AP*TP*GP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,5284
Polymers27,5284
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-23 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.056, 49.440, 95.194
Angle α, β, γ (deg.)90.000, 109.330, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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*AP*AP*AP*TP*CP*AP*TP*GP*C)-3')


Mass: 4263.804 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*TP*AP*TP*GP*AP*C)-3')


Mass: 4294.814 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.: 43 / 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: 3.11 Å3/Da / Density % sol: 60.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 200mM MgCl2, 0.1M Tris pH 5.8, 17.5% PEG 4000, 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: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.443→29.942 Å / Num. obs: 12413 / % possible obs: 97.33 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 18.49
Reflection shellResolution: 2.443→2.53 Å / Rmerge(I) obs: 0.539 / Num. unique obs: 980

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B8I

1b8i


Resolution: 2.443→29.942 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.34
RfactorNum. reflection% reflection
Rfree0.2522 1236 9.99 %
Rwork0.2228 --
obs0.2259 12378 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.31 Å2 / Biso mean: 45.5612 Å2 / Biso min: 18.63 Å2
Refinement stepCycle: final / Resolution: 2.443→29.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 568 0 43 1731
Biso mean---33.97 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071779
X-RAY DIFFRACTIONf_angle_d0.9032509
X-RAY DIFFRACTIONf_chiral_restr0.04265
X-RAY DIFFRACTIONf_plane_restr0.004223
X-RAY DIFFRACTIONf_dihedral_angle_d23.74702
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4431-2.54090.35681090.29421005111479
2.5409-2.65640.33281410.29321243138499
2.6564-2.79640.30241370.265312531390100
2.7964-2.97150.34681440.281212621406100
2.9715-3.20060.30081360.244612701406100
3.2006-3.52230.22821470.19711254140198
3.5223-4.03090.22221440.197712581402100
4.0309-5.07450.19551380.191912831421100
5.0745-29.94390.24391400.21541314145499
Refinement TLS params.Method: refined / Origin x: -18.1278 Å / Origin y: 1.8931 Å / Origin z: 119.8547 Å
111213212223313233
T0.2701 Å2-0.1014 Å20.008 Å2-0.256 Å2-0.014 Å2--0.2243 Å2
L2.7253 °2-0.3589 °2-0.949 °2-1.8931 °20.0244 °2--3.1262 °2
S-0.1913 Å °0.4201 Å °0.1058 Å °-0.3119 Å °0.1774 Å °-0.0278 Å °0.1328 Å °0.0932 Å °0.0272 Å °
Refinement TLS groupSelection details: all

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