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- PDB-3a01: Crystal structure of Aristaless and Clawless homeodomains bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3a01
TitleCrystal structure of Aristaless and Clawless homeodomains bound to DNA
Components
  • 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)-3'
  • 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)-3'
  • Homeobox protein aristaless
  • Homeodomain-containing protein
KeywordsGene Regulation/DNA / HOMEODOMAIN / PROTEIN-DNA COMPLEX / DNA-binding / Homeobox / Nucleus / Developmental protein / Gene Regulation-DNA COMPLEX
Function / homology
Function and homology information


elongation of arista core / leg disc development / antennal morphogenesis / imaginal disc-derived leg morphogenesis / chaeta development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription ...elongation of arista core / leg disc development / antennal morphogenesis / imaginal disc-derived leg morphogenesis / chaeta development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / nucleus
Similarity search - Function
T-cell leukemia homeobox protein 1/2/3 / OAR domain / OAR motif / OAR domain profile. / : / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain ...T-cell leukemia homeobox protein 1/2/3 / OAR domain / OAR motif / OAR domain profile. / : / Helix-turn-helix motif / 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 aristaless / Homeodomain-containing protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMiyazono, K. / Nagata, K. / Saigo, K. / Kojima, T. / Tanokura, M.
CitationJournal: Embo J. / Year: 2010
Title: Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless
Authors: Miyazono, K. / Zhi, Y. / Takamura, Y. / Nagata, K. / Saigo, K. / Kojima, T. / Tanokura, M.
History
DepositionFeb 28, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homeodomain-containing protein
B: Homeobox protein aristaless
C: 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)-3'
D: 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)-3'
E: Homeodomain-containing protein
F: Homeobox protein aristaless
G: 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)-3'
H: 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)59,8818
Polymers59,8818
Non-polymers00
Water00
1
A: Homeodomain-containing protein
B: Homeobox protein aristaless
C: 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)-3'
D: 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)29,9404
Polymers29,9404
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-25 kcal/mol
Surface area13040 Å2
MethodPISA
2
E: Homeodomain-containing protein
F: Homeobox protein aristaless
G: 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)-3'
H: 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)29,9404
Polymers29,9404
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-29 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.930, 85.400, 110.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Homeodomain-containing protein


Mass: 11191.974 Da / Num. of mol.: 2 / Fragment: Clawless Homeobox, residues 170-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: C15, CG7937 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VD99
#2: Protein Homeobox protein aristaless


Mass: 8335.609 Da / Num. of mol.: 2 / Fragment: Homeobox, residues 80-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: al, CG3935 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06453
#3: DNA chain 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)-3'


Mass: 5257.419 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: DNA chain 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)-3'


Mass: 5155.375 Da / Num. of mol.: 2 / Source method: obtained synthetically

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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: 2.8 Å3/Da / Density % sol: 56.06 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 18995

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3A02, 3A03, and 1PUF

3a02

3a03

1puf


Resolution: 2.7→19.65 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.793 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28275 1943 10.2 %RANDOM
Rwork0.22824 ---
obs0.23363 17051 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.7→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 1382 0 0 3668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213884
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7692.3895508
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.995259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49420.84131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.42415452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8371541
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022491
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21540
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22488
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 121 -
Rwork0.354 1242 -
obs--100 %

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