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- PDB-4xrs: Heterodimeric complex of transcription factors MEIS1 and DLX3 on ... -

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Basic information

Entry
Database: PDB / ID: 4xrs
TitleHeterodimeric complex of transcription factors MEIS1 and DLX3 on specific DNA
Components
  • (Homeobox protein ...) x 2
  • DNA (5'-D(P*AP*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*AP*C)-3')
  • DNA (5'-D(P*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*A)-3')
  • DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*TP*T)-3')
  • DNA (5'-D(P*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*T)-3')
KeywordsTRANSCRIPTION / heterodimer / DNA
Function / homology
Function and homology information


cell growth involved in cardiac muscle cell development / odontoblast differentiation / negative regulation of myeloid cell differentiation / lens morphogenesis in camera-type eye / chromatin => GO:0000785 / eye development / embryonic pattern specification / definitive hemopoiesis / megakaryocyte development / blood vessel development ...cell growth involved in cardiac muscle cell development / odontoblast differentiation / negative regulation of myeloid cell differentiation / lens morphogenesis in camera-type eye / chromatin => GO:0000785 / eye development / embryonic pattern specification / definitive hemopoiesis / megakaryocyte development / blood vessel development / odontogenesis of dentin-containing tooth / hemopoiesis / negative regulation of neuron differentiation / epithelial cell differentiation / locomotory behavior / animal organ morphogenesis / placenta development / brain development / 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 / sequence-specific DNA binding / transcription regulator complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Distal-less-like homeobox protein, N-terminal domain / Homeobox protein distal-less-like N terminal / Homeobox protein PKNOX/Meis, N-terminal / N-terminal of Homeobox Meis and PKNOX1 / Homeobox KN domain / Homeobox KN domain / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. ...Distal-less-like homeobox protein, N-terminal domain / Homeobox protein distal-less-like N terminal / Homeobox protein PKNOX/Meis, N-terminal / N-terminal of Homeobox Meis and PKNOX1 / Homeobox KN domain / Homeobox KN domain / Helix-turn-helix motif / 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 Meis1 / Homeobox protein DLX-3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsJorma, A. / Yin, Y. / Nitta, K.R. / Dave, K. / Enge, M. / Kivioja, T. / Popov, A. / Morgunova, E. / 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 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_seq_map_depositor_info
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Jan 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*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*A)-3')
D: DNA (5'-D(P*AP*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*AP*C)-3')
E: DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*TP*T)-3')
L: DNA (5'-D(P*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*T)-3')
A: Homeobox protein Meis1
B: Homeobox protein Meis1
G: Homeobox protein DLX-3
I: Homeobox protein DLX-3


Theoretical massNumber of molelcules
Total (without water)47,7178
Polymers47,7178
Non-polymers00
Water00
1
M: DNA (5'-D(P*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*A)-3')
L: DNA (5'-D(P*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*T)-3')
A: Homeobox protein Meis1
G: Homeobox protein DLX-3


Theoretical massNumber of molelcules
Total (without water)23,4054
Polymers23,4054
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-18 kcal/mol
Surface area14060 Å2
MethodPISA
2
D: DNA (5'-D(P*AP*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*AP*C)-3')
E: DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*TP*T)-3')
B: Homeobox protein Meis1
I: Homeobox protein DLX-3


Theoretical massNumber of molelcules
Total (without water)24,3124
Polymers24,3124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-15 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.636, 69.845, 116.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 4 types, 4 molecules MDEL

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


Mass: 4527.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*AP*AP*TP*TP*AP*TP*CP*CP*TP*GP*TP*CP*AP*AP*C)-3')


Mass: 5130.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*TP*T)-3')


Mass: 5585.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*TP*TP*GP*AP*CP*AP*GP*GP*AP*TP*AP*AP*TP*TP*GP*T)-3')


Mass: 5281.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Homeobox protein ... , 2 types, 4 molecules ABGI

#5: Protein Homeobox protein Meis1


Mass: 6914.002 Da / Num. of mol.: 2 / Fragment: UNP residues 283-340
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
#6: Protein Homeobox protein DLX-3


Mass: 6681.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLX3 / Plasmid: PETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O60479

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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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 8000, TRIS, Magnesium chloride, buthanol / PH range: 7 - 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 315 / Detector: CCD / Date: Jun 14, 2014
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.08
ReflectionResolution: 2.9→50 Å / Num. all: 46033 / Num. obs: 11191 / % possible obs: 90.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 109.76 Å2 / Rmerge(I) obs: 0.0608 / Net I/σ(I): 13.08
Reflection shellResolution: 2.964→3.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.0608 / Mean I/σ(I) obs: 0.63 / % possible all: 88.39

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXphenix.refine: 1.9_1692refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K2A, 2DJN

3k2a

2djn


Resolution: 3.5→49.314 Å / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 45.01 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.3591 651 5.33 %random
Rwork0.3305 11570 --
obs0.3427 6829 88.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 232.96 Å2 / Biso mean: 136.3207 Å2 / Biso min: 82.43 Å2
Refinement stepCycle: final / Resolution: 3.5→49.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 1352 0 0 3247
Num. residues----292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073471
X-RAY DIFFRACTIONf_angle_d1.1794961
X-RAY DIFFRACTIONf_chiral_restr0.183550
X-RAY DIFFRACTIONf_plane_restr0.007398
X-RAY DIFFRACTIONf_dihedral_angle_d27.2141390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5029-3.85520.46851630.38232894305784
3.8552-4.41270.42721530.38192941309485
4.4127-5.55780.40491570.36742890304784
5.5578-44.77040.30861390.30222845298482

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