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- PDB-5ego: HOXB13-MEIS1 heterodimer bound to methylated DNA -

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Basic information

Entry
Database: PDB / ID: 5ego
TitleHOXB13-MEIS1 heterodimer bound to methylated DNA
Components
  • DNA (5'-D(*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*TP*GP*TP*CP*AP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*G)-3')
  • Homeobox protein Hox-B13
  • Homeobox protein Meis1
KeywordsTRANSCRIPTION / transcription factor / heterodimer / complex / bound to DNA
Function / homology
Function and homology information


epithelial cell maturation involved in prostate gland development / cell growth involved in cardiac muscle cell development / negative regulation of myeloid cell differentiation / lens morphogenesis in camera-type eye / eye development / embryonic pattern specification / methyl-CpG binding / definitive hemopoiesis / regulation of growth / megakaryocyte development ...epithelial cell maturation involved in prostate gland development / cell growth involved in cardiac muscle cell development / negative regulation of myeloid cell differentiation / lens morphogenesis in camera-type eye / eye development / embryonic pattern specification / methyl-CpG binding / definitive hemopoiesis / regulation of growth / megakaryocyte development / response to testosterone / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / hemopoiesis / negative regulation of neuron differentiation / epidermis development / locomotory behavior / animal organ morphogenesis / brain development / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / 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 / angiogenesis / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Homeobox protein PKNOX/Meis, N-terminal / N-terminal of Homeobox Meis and PKNOX1 / Homeobox protein Hox1A3 N-terminal / Hox protein A13 N terminal / Homeobox KN domain / Homeobox KN domain / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. ...Homeobox protein PKNOX/Meis, N-terminal / N-terminal of Homeobox Meis and PKNOX1 / Homeobox protein Hox1A3 N-terminal / Hox protein A13 N terminal / Homeobox KN domain / Homeobox KN domain / 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 Meis1 / Homeobox protein Hox-B13
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsMorgunova, E. / Yin, Y. / Jolma, A. / Popov, A. / Taipale, J.
CitationJournal: Science / Year: 2017
Title: Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Authors: Yin, Y. / Morgunova, E. / Jolma, A. / Kaasinen, E. / Sahu, B. / Khund-Sayeed, S. / Das, P.K. / Kivioja, T. / Dave, K. / Zhong, F. / Nitta, K.R. / Taipale, M. / Popov, A. / Ginno, P.A. / ...Authors: Yin, Y. / Morgunova, E. / Jolma, A. / Kaasinen, E. / Sahu, B. / Khund-Sayeed, S. / Das, P.K. / Kivioja, T. / Dave, K. / Zhong, F. / Nitta, K.R. / Taipale, M. / Popov, A. / Ginno, P.A. / Domcke, S. / Yan, J. / Schubeler, D. / Vinson, C. / Taipale, J.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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 Meis1
D: DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*G)-3')
E: DNA (5'-D(*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*TP*GP*TP*CP*AP*AP*C)-3')
B: Homeobox protein Hox-B13


Theoretical massNumber of molelcules
Total (without water)25,4564
Polymers25,4564
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-14 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.976, 51.480, 113.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Homeobox protein Meis1 /


Mass: 6756.834 Da / Num. of mol.: 1 / Fragment: UNP residues 279-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEIS1 / Plasmid: pETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O00470
#2: DNA chain DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*G)-3')


Mass: 5600.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*TP*GP*TP*CP*AP*AP*C)-3')


Mass: 5458.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein Homeobox protein Hox-B13 /


Mass: 7640.061 Da / Num. of mol.: 1 / Fragment: UNP residues 217-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOXB13 / Plasmid: pETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q92826
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 5000, potassium chloride, magnesium chloride, Tris, PEG 400
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 25, 2015
RadiationMonochromator: Si(111) and Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.54→40 Å / Num. obs: 8290 / % possible obs: 98.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.5
Reflection shellResolution: 2.54→2.63 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 1.6 / % possible all: 98.8

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XRM

4xrm


Resolution: 2.54→38.544 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 379 4.61 %random
Rwork0.2279 7835 --
obs0.2296 8214 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.57 Å2 / Biso mean: 70.1019 Å2 / Biso min: 49.36 Å2
Refinement stepCycle: final / Resolution: 2.54→38.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 737 0 20 1770
Biso mean---60.53 -
Num. residues----156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061855
X-RAY DIFFRACTIONf_angle_d1.0652644
X-RAY DIFFRACTIONf_chiral_restr0.04290
X-RAY DIFFRACTIONf_plane_restr0.005209
X-RAY DIFFRACTIONf_dihedral_angle_d27.895746
LS refinement shellResolution: 2.5401→2.9076 Å
RfactorNum. reflection% reflection
Rfree0.4971 130 -
Rwork0.3921 2555 -
obs--98 %

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