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- PDB-5zjt: Structure of AbdB/Exd complex bound to a 'Black14' DNA sequence -

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Basic information

Entry
Database: PDB / ID: 5zjt
TitleStructure of AbdB/Exd complex bound to a 'Black14' DNA sequence
Components
  • DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*AP*AP*AP*TP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*AP*TP*TP*TP*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 / gonadal mesoderm development / oenocyte development / : / female genitalia development / open tracheal system development / somatic muscle development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / polytene chromosome band / negative regulation of female receptivity / 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 / germ cell migration / peripheral nervous system development / midgut development / transcription factor binding / neuron development / embryonic organ development / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription coregulator activity / animal organ morphogenesis / brain development / RNA polymerase II transcription regulator complex / male gonad development / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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. / Homeodomain ...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 / Resolution: 2.4 Å
AuthorsZeiske, T. / Baburajendran, N. / 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 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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*TP*AP*TP*CP*AP*TP*GP*C)-3')
D: DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*AP*AP*AP*TP*GP*AP*C)-3')
E: Homeobox protein abdominal-B
G: DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*AP*AP*AP*TP*GP*AP*C)-3')
H: DNA (5'-D(*GP*TP*CP*AP*TP*TP*TP*AP*TP*CP*AP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)46,2837
Polymers46,2837
Non-polymers00
Water1,44180
1
A: Homeobox protein abdominal-B
B: Homeobox protein extradenticle
C: DNA (5'-D(*GP*TP*CP*AP*TP*TP*TP*AP*TP*CP*AP*TP*GP*C)-3')
D: DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*AP*AP*AP*TP*GP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,5284
Polymers27,5284
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-24 kcal/mol
Surface area11640 Å2
MethodPISA
2
E: Homeobox protein abdominal-B
G: DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*AP*AP*AP*TP*GP*AP*C)-3')
H: DNA (5'-D(*GP*TP*CP*AP*TP*TP*TP*AP*TP*CP*AP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)18,7543
Polymers18,7543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-20 kcal/mol
Surface area8150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.440, 45.630, 66.860
Angle α, β, γ (deg.)99.050, 100.370, 114.180
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 10195.751 Da / Num. of mol.: 2
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*TP*AP*TP*CP*AP*TP*GP*C)-3')


Mass: 4245.776 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#4: DNA chain DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*AP*AP*AP*TP*GP*AP*C)-3')


Mass: 4312.842 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M Sodium citrate pH 5.3, 25% PEG 3350

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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: Apr 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→63.551 Å / Num. obs: 16923 / % possible obs: 93.06 % / Redundancy: 2 % / Biso Wilson estimate: 27.35 Å2 / Net I/σ(I): 6.8
Reflection shellResolution: 2.4→2.486 Å

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 2.4→63.551 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.92
RfactorNum. reflection% reflection
Rfree0.2759 1682 9.95 %
Rwork0.2324 --
obs0.2367 16909 92.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.79 Å2 / Biso mean: 36.7017 Å2 / Biso min: 5.52 Å2
Refinement stepCycle: final / Resolution: 2.4→63.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 1139 0 80 2852
Biso mean---27.22 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032942
X-RAY DIFFRACTIONf_angle_d0.4684188
X-RAY DIFFRACTIONf_chiral_restr0.02443
X-RAY DIFFRACTIONf_plane_restr0.001340
X-RAY DIFFRACTIONf_dihedral_angle_d23.6641186
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.47060.35391320.29471258139092
2.4706-2.55040.34021400.27721277141793
2.5504-2.64150.33741480.28241238138693
2.6415-2.74730.30771330.26311262139593
2.7473-2.87230.28751480.26991298144694
2.8723-3.02380.34731340.26871288142294
3.0238-3.21320.29111350.22681259139493
3.2132-3.46130.24371440.19051258140292
3.4613-3.80960.24671460.20711287143393
3.8096-4.36070.24951390.20611267140694
4.3607-5.49360.24811350.21611257139292
5.4936-63.57320.26071480.23871278142694
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.90950.4603-0.33511.2338-0.20122.98-0.06450.3122-0.148-0.07970.0255-0.2161-0.0650.29270.03620.11430.0156-0.01040.10480.02560.220422.3594-15.1651-131.3541
21.725-0.2980.97672.87970.27793.45090.125-0.1264-0.04260.519-0.18130.6728-0.2443-0.75080.11010.3213-0.00570.05470.3755-0.01250.21836.1308-8.169-107.9387
30.45290.5781-0.08570.96940.48591.542-0.01330.150.2470.1781-0.29220.2082-0.2731-0.0832-0.31870.37360.1233-0.05170.19810.05250.376613.6768-7.8716-120.5942
42.00880.3488-0.63721.82390.64582.1351-0.005-0.12070.22640.3823-0.21-0.2475-0.269-0.13420.2010.31140.0305-0.0810.20650.02650.449315.4305-7.61-118.7888
53.80290.9-0.37534.35310.09223.3443-0.0112-0.08480.0130.2140.00350.4574-0.00310.0177-0.02840.1529-0.0383-0.01980.151-0.01010.2608-9.27734.7237-136.0819
63.98070.49070.44041.1785-0.28210.4494-0.27780.15770.031-0.17690.18320.17780.13560.3169-0.01370.1544-0.02820.00360.3853-0.04370.2787-4.34741.4591-148.8043
71.4361-0.4446-0.41732.5516-0.78622.0145-0.4630.6988-0.2106-0.14150.3245-0.27070.34640.26220.08190.23260.00020.02090.4403-0.06570.362-4.66430.738-151.2029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA10 - 77
2X-RAY DIFFRACTION2chain BB3 - 74
3X-RAY DIFFRACTION3chain CC1 - 14
4X-RAY DIFFRACTION4chain DD1 - 14
5X-RAY DIFFRACTION5chain EE21 - 78
6X-RAY DIFFRACTION6chain GG-1 - 12
7X-RAY DIFFRACTION7chain HH3 - 16

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