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- PDB-1puf: Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA -

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Basic information

Entry
Database: PDB / ID: 1puf
TitleCrystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA
Components
  • 5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*AP*CP*GP*CP*T)-3'
  • 5'-D(*TP*AP*GP*CP*GP*TP*CP*GP*TP*AP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3'
  • Homeobox protein Hox-A9
  • Pre-B-cell leukemia transcription factor-1
KeywordsTranscription/DNA / Homeodomian / Protein-DNA complex / Hox Hexapeptide / TALE homeodomain / Homeodomain interaction / Transcription-DNA COMPLEX
Function / homology
Function and homology information


urogenital system development / natural killer cell differentiation / negative regulation of myeloid cell differentiation / proximal/distal pattern formation / embryonic skeletal system development / sex differentiation / Transcriptional regulation of pluripotent stem cells / eye development / steroid biosynthetic process / mammary gland development ...urogenital system development / natural killer cell differentiation / negative regulation of myeloid cell differentiation / proximal/distal pattern formation / embryonic skeletal system development / sex differentiation / Transcriptional regulation of pluripotent stem cells / eye development / steroid biosynthetic process / mammary gland development / definitive hemopoiesis / embryonic forelimb morphogenesis / embryonic limb morphogenesis / endothelial cell activation / anterior/posterior pattern specification / embryonic hemopoiesis / NOTCH3 Intracellular Domain Regulates Transcription / adrenal gland development / branching involved in ureteric bud morphogenesis / positive regulation of stem cell proliferation / uterus development / regulation of ossification / single fertilization / negative regulation of neuron differentiation / embryonic organ development / neuron development / spleen development / positive regulation of G2/M transition of mitotic cell cycle / thymus development / transcription coregulator binding / animal organ morphogenesis / transcription corepressor binding / stem cell proliferation / negative regulation of DNA-binding transcription factor activity / brain development / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II transcription regulator complex / male gonad development / G2/M transition of mitotic cell cycle / sequence-specific double-stranded DNA binding / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / spermatogenesis / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Hox9, N-terminal activation domain / Homeobox protein HXA9/HXB9/HXC9 / : / Hox9 activation region / PBX, PBC domain / PBC domain / PBC domain profile. / : / Homeobox KN domain / Homeobox KN domain ...Hox9, N-terminal activation domain / Homeobox protein HXA9/HXB9/HXC9 / : / Hox9 activation region / 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 Hox-A9 / Pre-B-cell leukemia transcription factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLaronde-Leblanc, N.A. / Wolberger, C.
CitationJournal: Genes Dev. / Year: 2003
Title: STRUCTURE OF HOXA9 AND PBX1 BOUND TO DNA: HOX HEXAPEPTIDE AND DNA RECOGNITION ANTERIOR TO POSTERIOR
Authors: LARONDE-LEBLANC, N.A. / Wolberger, C.
History
DepositionJun 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
D: 5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*AP*CP*GP*CP*T)-3'
E: 5'-D(*TP*AP*GP*CP*GP*TP*CP*GP*TP*AP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3'
A: Homeobox protein Hox-A9
B: Pre-B-cell leukemia transcription factor-1


Theoretical massNumber of molelcules
Total (without water)30,6604
Polymers30,6604
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.769, 114.853, 108.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain 5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*AP*CP*GP*CP*T)-3'


Mass: 6083.953 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*AP*GP*CP*GP*TP*CP*GP*TP*AP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3'


Mass: 6182.029 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Homeobox protein Hox-A9 / Hox-1.7


Mass: 9646.336 Da / Num. of mol.: 1 / Fragment: residues 193-269
Source method: isolated from a genetically manipulated source
Details: Homeodomain / Source: (gene. exp.) Mus musculus (house mouse) / Gene: HOXA9 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) Codon + -RIL / References: UniProt: P09631
#4: Protein Pre-B-cell leukemia transcription factor-1 / Homeobox protein PBX1 / Homeobox protein PRL


Mass: 8747.872 Da / Num. of mol.: 1 / Fragment: residues 233-305
Source method: isolated from a genetically manipulated source
Details: Homeodomain / Source: (gene. exp.) Homo sapiens (human) / Gene: PBX1 / Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P40424
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 292 K / pH: 7.5
Details: PEG 4000, hepes, cobaltic hexamine, dithiothrietol, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 7.50
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2hepes11
3cobaltic hexamine11
4dithiothrietol11
5EDTA11
6H2O11
7PEG 400012
8hepes12
9cobaltic hexamine12
10EDTA12
11dithiothrietol12
12H2O12
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMHEPES1droppH7.5
21 mMdithiothreitol1drop
31 mMEDTA1drop
411 %PEG10001reservoir
5100 mMTris1reservoirpH8.0
64 mMcobalt hexamine1reservoir
71
81
91
101
111
121

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9116
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 27, 2000
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 28839 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 31.6 Å2 / Rsym value: 0.065 / Net I/σ(I): 22.3
Reflection shellResolution: 1.9→20 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.26 / % possible all: 94.1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 95.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 94.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B72

1b72


Resolution: 1.9→19.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1537852.39 / Data cutoff high rms absF: 1537852.39 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2873 10 %RANDOM IN CNS
Rwork0.233 ---
obs0.233 28839 95.6 %-
all-30169 --
Displacement parametersBiso mean: 48.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å20 Å20 Å2
2---8.53 Å20 Å2
3---10.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 814 0 247 2329
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 456 9.9 %
Rwork0.322 4155 -
obs--93.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION_REP.PARAMION.TOP
Software
*PLUS
Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 9.5 % / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.37

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