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- PDB-4xrm: homodimer of TALE type homeobox transcription factor MEIS1 comple... -

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Basic information

Entry
Database: PDB / ID: 4xrm
Titlehomodimer of TALE type homeobox transcription factor MEIS1 complexes with specific DNA
Components
  • DNA (5'-D(P*AP*GP*CP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*G)-3')
  • DNA (5'-D(P*TP*CP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*GP*C)-3')
  • Homeobox protein Meis2
KeywordsTRANSCRIPTION / TALE homeobox / MEIS / Complex / DNA
Function / homology
Function and homology information


positive regulation of cardiac muscle myoblast proliferation / negative regulation of myeloid cell differentiation / eye development / response to growth factor / embryonic pattern specification / pancreas development / transcription factor binding / response to mechanical stimulus / positive regulation of mitotic cell cycle / animal organ morphogenesis ...positive regulation of cardiac muscle myoblast proliferation / negative regulation of myeloid cell differentiation / eye development / response to growth factor / embryonic pattern specification / pancreas development / transcription factor binding / response to mechanical stimulus / positive regulation of mitotic cell cycle / animal organ morphogenesis / brain development / visual learning / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / chromatin / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Homeobox protein PKNOX/Meis, N-terminal / TALE/MEIS homeobox family N-terminal domain / : / Homeobox KN domain / Homeobox KN domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily ...Homeobox protein PKNOX/Meis, N-terminal / TALE/MEIS homeobox family N-terminal domain / : / Homeobox KN domain / Homeobox KN domain / '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
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMorgunova, E. / Jorma, A. / Yin, Y. / Nitta, K.R. / Dave, K. / Enge, M. / Kivioja, T. / Popov, A. / Taipale, J.
CitationJournal: Nature / Year: 2015
Title: DNA-dependent formation of transcription factor pairs alters their binding specificity.
Authors: Jolma, A. / Yin, Y. / Nitta, K.R. / Dave, K. / Popov, A. / Taipale, M. / Enge, M. / Kivioja, T. / Morgunova, E. / Taipale, J.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Jan 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
M: DNA (5'-D(P*AP*GP*CP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*G)-3')
L: DNA (5'-D(P*TP*CP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*GP*C)-3')
A: Homeobox protein Meis2
B: Homeobox protein Meis2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6946
Polymers25,4504
Non-polymers2442
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-15 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.620, 79.280, 98.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 5236.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*TP*CP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*GP*C)-3')


Mass: 5178.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Homeobox protein Meis2 / Meis1-related protein 1


Mass: 7517.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEIS2, MRG1 / Plasmid: PETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 pLysS / References: UniProt: O14770
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PME 5000, Tris, PEG 400, magnesium chloride / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2014
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 149060 / Num. obs: 36011 / % possible obs: 97.28 % / Redundancy: 4.1 % / Biso Wilson estimate: 25.92 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 14.84
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7128 / Mean I/σ(I) obs: 1.56 / % possible all: 93.87

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
RESOLVEmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
DNAdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k2a

3k2a


Resolution: 1.6→19.83 Å / FOM work R set: 0.7632 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 720 2 %
Rwork0.1767 35231 -
obs0.1773 35951 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196.26 Å2 / Biso mean: 42.14 Å2 / Biso min: 20.69 Å2
Refinement stepCycle: final / Resolution: 1.6→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1016 697 40 309 2062
Biso mean--38.23 48.07 -
Num. residues----157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051835
X-RAY DIFFRACTIONf_angle_d0.792629
X-RAY DIFFRACTIONf_chiral_restr0.033292
X-RAY DIFFRACTIONf_plane_restr0.004214
X-RAY DIFFRACTIONf_dihedral_angle_d24.917730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.72350.29991420.27916906X-RAY DIFFRACTION96
1.7235-1.89680.25731440.23477060X-RAY DIFFRACTION98
1.8968-2.1710.22921450.19367094X-RAY DIFFRACTION99
2.171-2.73410.21041440.18567053X-RAY DIFFRACTION97
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)
10.63710.43350.03710.8198-0.45822.15310.0582-0.0293-0.03520.0817-0.062-0.01290.1322-0.038300.27550.0234-0.03320.26890.01350.272612.044715.892118.3811
21.33160.81280.03472.0915-0.53313.2115-0.01440.0229-0.0431-0.08420.0344-0.088-0.0320.0379-0.00070.2481-0.00780.01560.2491-0.0410.270616.087626.1891-12.243
32.0845-0.1605-0.41531.0412-1.2721.68520.19090.0224-0.11180.03910.0047-0.17530.18880.00580.00260.25050.02910.03870.2406-0.0130.289718.232619.5480.9382
41.4897-0.2283-0.71051.1856-1.11771.6260.0686-0.1702-0.0393-0.13130.0802-0.1666-0.10580.2190.00190.23270.0147-0.03820.2758-0.00040.279718.397620.02885.1534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allchain 'L' and (resid 21 through 37)L0
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 64 )B0
3X-RAY DIFFRACTION3chain 'M' and (resid 1 through 17 )M0
4X-RAY DIFFRACTION4chain 'L' and (resid 21 through 37)L0

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