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- PDB-1b72: PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1b72
TitlePBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX
Components
  • DNA (5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*GP*AP*TP*CP*GP*GP*CP*TP*G)-3')
  • DNA (5'-D(*TP*CP*AP*GP*CP*CP*GP*AP*TP*CP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3')
  • PROTEIN (HOMEOBOX PROTEIN HOX-B1)
  • PROTEIN (PBX1)
KeywordsPROTEIN/DNA / HOMEODOMAIN / DNA / COMPLEX / DNA-BINDING PROTEIN / PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


rhombomere 4 development / rhombomere 5 development / facial nucleus development / anatomical structure formation involved in morphogenesis / urogenital system development / facial nerve structural organization / embryonic skeletal system morphogenesis / proximal/distal pattern formation / natural killer cell differentiation / embryonic skeletal system development ...rhombomere 4 development / rhombomere 5 development / facial nucleus development / anatomical structure formation involved in morphogenesis / urogenital system development / facial nerve structural organization / embryonic skeletal system morphogenesis / proximal/distal pattern formation / natural killer cell differentiation / embryonic skeletal system development / sex differentiation / Transcriptional regulation of pluripotent stem cells / eye development / pattern specification process / steroid biosynthetic process / embryonic limb morphogenesis / anterior/posterior pattern specification / embryonic hemopoiesis / NOTCH3 Intracellular Domain Regulates Transcription / adrenal gland development / branching involved in ureteric bud morphogenesis / negative regulation of neuron differentiation / positive regulation of stem cell proliferation / regulation of ossification / positive regulation of G2/M transition of mitotic cell cycle / embryonic organ development / neuron development / negative regulation of DNA-binding transcription factor activity / spleen development / thymus development / animal organ morphogenesis / transcription corepressor binding / stem cell proliferation / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / G2/M transition of mitotic cell cycle / RNA polymerase II transcription regulator complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / 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 / protein domain specific binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Homeobox protein Hox-A1/B1/D1 / 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-A1/B1/D1 / 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-B1 / Pre-B-cell leukemia transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.35 Å
AuthorsPiper, D.E. / Batchelor, A.H. / Chang, C.-P. / Cleary, M.L. / Wolberger, C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation.
Authors: Piper, D.E. / Batchelor, A.H. / Chang, C.P. / Cleary, M.L. / Wolberger, C.
History
DepositionJan 27, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*GP*AP*TP*CP*GP*GP*CP*TP*G)-3')
E: DNA (5'-D(*TP*CP*AP*GP*CP*CP*GP*AP*TP*CP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3')
A: PROTEIN (HOMEOBOX PROTEIN HOX-B1)
B: PROTEIN (PBX1)


Theoretical massNumber of molelcules
Total (without water)33,7834
Polymers33,7834
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.670, 64.580, 81.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*GP*AP*TP*CP*GP*GP*CP*TP*G)-3')


Mass: 6139.976 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*CP*AP*GP*CP*CP*GP*AP*TP*CP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3')


Mass: 6126.994 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (HOMEOBOX PROTEIN HOX-B1)


Mass: 11443.128 Da / Num. of mol.: 1 / Fragment: HEXAPEPTIDE, HOMEODOMAIN / Mutation: 1 RESIDUE (MET) ADDED TO N-TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOXB-1 / Plasmid: PET11-D T7 PROMOTER / Gene (production host): HOXB-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P14653
#4: Protein PROTEIN (PBX1)


Mass: 10073.342 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PBX1 / Plasmid: PET11-D T7 PROMOTER / Gene (production host): PBX1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P40424
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 8 / Details: pH 8.0
Components of the solutions
IDNameCrystal-IDSol-ID
1TRIS11
2PEG 100011
3CO(NH3)611
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: equal volume of protein and reservoir solution were used for the drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mMHEPES1drop
21 mMEDTA1drop
31 mMdithiothreitol1drop
40.001 %1dropNaN3
5100 mMTris-HCl1reservoir
65 mMcobaltic hexamine chloride1reservoir
712 %PEG10001reservoir
8protein-DNA comples1dropprotein was mixed with lyophilized DNA in a molar ration of 1:1:1.5 HoxB1:Pbx1:DNA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 15, 1998 / Details: SPHERICAL RH COATED
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 13735 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 44 Å2 / Rsym value: 0.033 / Net I/σ(I): 27.2
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 7.7 / Rsym value: 0.248 / % possible all: 99.7
Reflection
*PLUS
Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.248

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.35→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 1033240 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1368 10.2 %RANDOM
Rwork0.243 ---
obs0.243 13418 99.7 %-
all-13418 --
Displacement parametersBiso mean: 53.2 Å2
Baniso -1Baniso -2Baniso -3
1--18.8 Å20 Å20 Å2
2--17.53 Å20 Å2
3---1.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 814 0 61 2010
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it4.042
X-RAY DIFFRACTIONc_scangle_it5.092.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 209 9.7 %
Rwork0.324 1955 -
obs--99.8 %
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.PARAM
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03
LS refinement shell
*PLUS
Rfactor obs: 0.324

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