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- PDB-5eg0: HOXB13-MEIS1 heterodimer bound to DNA -

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Basic information

Entry
Database: PDB / ID: 5eg0
TitleHOXB13-MEIS1 heterodimer bound to DNA
Components
  • DNA (5'-D(*CP*CP*TP*CP*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*CP*GP*AP*GP*G)-3')
  • Homeobox protein Hox-B13
  • Homeobox protein Meis2
KeywordsTRANSCRIPTION / transcription factor / heterodimer / complex / bound to DNA
Function / homology
Function and homology information


positive regulation of cardiac muscle myoblast proliferation / epithelial cell maturation involved in prostate gland development / negative regulation of myeloid cell differentiation / eye development / response to growth factor / embryonic pattern specification / pancreas development / methyl-CpG binding / regulation of growth / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...positive regulation of cardiac muscle myoblast proliferation / epithelial cell maturation involved in prostate gland development / negative regulation of myeloid cell differentiation / eye development / response to growth factor / embryonic pattern specification / pancreas development / methyl-CpG binding / regulation of growth / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / response to testosterone / transcription factor binding / epidermis development / response to mechanical stimulus / positive regulation of mitotic cell cycle / animal organ morphogenesis / brain development / visual learning / response to wounding / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin / perinuclear region of cytoplasm / 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 / TALE/MEIS homeobox family N-terminal domain / Homeobox protein Hox1A3 N-terminal / : / Hox protein A13 N terminal / : / Homeobox KN domain / Homeobox KN domain / Homeobox, conserved site / 'Homeobox' domain signature. ...Homeobox protein PKNOX/Meis, N-terminal / TALE/MEIS homeobox family N-terminal domain / 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 Meis2 / Homeobox protein Hox-B13
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å
AuthorsMorgunova, E. / Yin, Y. / Jolma, A. / Popov, A. / Taipale, J.
CitationJournal: Nature / Year: 2025
Title: DNA-guided transcription factor interactions extend human gene regulatory code.
Authors: Xie, Z. / Sokolov, I. / Osmala, M. / Yue, X. / Bower, G. / Pett, J.P. / Chen, Y. / Wang, K. / Cavga, A.D. / Popov, A. / Teichmann, S.A. / Morgunova, E. / Kvon, E.Z. / Yin, Y. / Taipale, J.
History
DepositionOct 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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
Revision 1.2Apr 23, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homeobox protein Meis2
D: DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*G)-3')
E: DNA (5'-D(*CP*CP*TP*CP*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)25,1244
Polymers25,1244
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-22 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.726, 56.332, 115.152
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 Homeobox protein Meis2 / Meis1-related protein 1


Mass: 6680.738 Da / Num. of mol.: 1 / Fragment: UNP residues 284-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEIS2, MRG1 / Plasmid: pETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O14770
#2: DNA chain DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*G)-3')


Mass: 5586.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*TP*GP*TP*CP*AP*AP*C)-3')


Mass: 5444.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein Homeobox protein Hox-B13


Mass: 7411.749 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


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 5000, potassium chloride, magnesium chloride, pentanol
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2014
RadiationMonochromator: Si(111) and Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2.97→40 Å / Num. obs: 6006 / % possible obs: 99 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 3.7
Reflection shellResolution: 2.97→3.13 Å / Redundancy: 5 % / Rmerge(I) obs: 2.77 / Mean I/σ(I) obs: 0.4 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XRM

4xrm


Resolution: 3.101→19.946 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3224 485 5.2 %random
Rwork0.2855 ---
obs0.2876 9326 98.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.101→19.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms979 735 0 29 1743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051813
X-RAY DIFFRACTIONf_angle_d0.8272593
X-RAY DIFFRACTIONf_dihedral_angle_d26.294746
X-RAY DIFFRACTIONf_chiral_restr0.036288
X-RAY DIFFRACTIONf_plane_restr0.004203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1005-3.5470.38821500.39062924X-RAY DIFFRACTION97
3.547-4.46060.35831800.33412925X-RAY DIFFRACTION99
4.4606-19.94620.2661550.21192992X-RAY DIFFRACTION99
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)
10.07630.0049-0.00680.06380.01090.0238-0.0770.1860.0979-0.03470.17780.19870.0569-0.18050.03190.3858-0.0544-0.02670.50890.14710.378614.0795-12.1021-20.6674
20.2160.4887-0.16651.0897-0.41750.3355-0.24970.13790.3671-0.06430.6856-0.0754-0.0145-0.2310.22530.66370.21810.01061.2857-0.02010.31757.685-0.9248-33.0833
30.1429-0.1180.01690.0787-0.01760.0806-0.0880.06150.245-0.54360.55490.0087-0.5145-0.91470.09771.1-0.07630.03220.80260.1670.28247.23671.4291-32.5406
40.24840.2190.07460.19160.12561.2619-0.09530.08580.0938-0.12690.3442-0.23720.35130.13130.23570.2204-0.26020.06660.5277-0.11250.356720.2611-0.8486-46.5463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 279 through 334 )
2X-RAY DIFFRACTION2chain 'D' and (resid 20 through 37)
3X-RAY DIFFRACTION3chain 'E' and (resid 1 through 18)
4X-RAY DIFFRACTION4chain 'B' and (resid 217 through 277 )

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