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- PDB-8osb: TWIST1-TCF4-ALX4 complex on specific DNA -

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Basic information

Entry
Database: PDB / ID: 8osb
TitleTWIST1-TCF4-ALX4 complex on specific DNA
Components
  • (DNA (25-MER)) x 2
  • Homeobox protein aristaless-like 4
  • Transcription factor 4
  • Twist-related protein 1
KeywordsTRANSCRIPTION / transcription factor / complex with DNA
Function / homology
Function and homology information


embryonic camera-type eye formation / cell proliferation involved in heart valve development / positive regulation of endocardial cushion to mesenchymal transition involved in heart valve formation / cranial suture morphogenesis / negative regulation of double-strand break repair / HMG box domain binding / negative regulation of skeletal muscle tissue development / positive regulation of DNA-templated transcription initiation / negative regulation of peroxisome proliferator activated receptor signaling pathway / protein-DNA complex assembly ...embryonic camera-type eye formation / cell proliferation involved in heart valve development / positive regulation of endocardial cushion to mesenchymal transition involved in heart valve formation / cranial suture morphogenesis / negative regulation of double-strand break repair / HMG box domain binding / negative regulation of skeletal muscle tissue development / positive regulation of DNA-templated transcription initiation / negative regulation of peroxisome proliferator activated receptor signaling pathway / protein-DNA complex assembly / beta-catenin-TCF7L2 complex / bHLH transcription factor binding / negative regulation of macrophage cytokine production / cardiac neural crest cell migration involved in outflow tract morphogenesis / beta-catenin-TCF complex / positive regulation of transcription regulatory region DNA binding / mitral valve morphogenesis / embryonic skeletal system morphogenesis / developmental process / Transcriptional regulation by RUNX2 / positive regulation of fatty acid beta-oxidation / regulation of bone mineralization / embryonic cranial skeleton morphogenesis / positive regulation of monocyte chemotactic protein-1 production / TGFBR3 expression / embryonic forelimb morphogenesis / digestive tract development / outer ear morphogenesis / aortic valve morphogenesis / embryonic hindlimb morphogenesis / anterior/posterior pattern specification / endocardial cushion morphogenesis / DNA-binding transcription repressor activity / positive regulation of cell motility / embryonic digit morphogenesis / muscle organ development / Myogenesis / E-box binding / eyelid development in camera-type eye / negative regulation of DNA damage response, signal transduction by p53 class mediator / roof of mouth development / TFIIB-class transcription factor binding / negative regulation of cellular senescence / negative regulation of tumor necrosis factor production / hair follicle development / negative regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / cis-regulatory region sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / energy homeostasis / positive regulation of neuron differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of miRNA transcription / ossification / transcription coregulator binding / positive regulation of epithelial cell proliferation / post-embryonic development / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neural tube closure / cellular response to growth factor stimulus / beta-catenin binding / positive regulation of interleukin-6 production / histone deacetylase binding / neuron migration / positive regulation of angiogenesis / Regulation of RUNX2 expression and activity / positive regulation of tumor necrosis factor production / osteoblast differentiation / sequence-specific double-stranded DNA binding / rhythmic process / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / DNA-binding transcription factor binding / cellular response to hypoxia / transcription regulator complex / in utero embryonic development / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / : / OAR domain / OAR motif / OAR domain profile. / : / : / Homeobox, conserved site / Helix-loop-helix DNA-binding domain / 'Homeobox' domain signature. ...: / : / OAR domain / OAR motif / OAR domain profile. / : / : / Homeobox, conserved site / Helix-loop-helix DNA-binding domain / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor 4 / Twist-related protein 1 / Homeobox protein aristaless-like 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMorgunova, E. / Kim, S. / Popov, A. / Wysocka, J. / Taipale, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2024
Title: DNA-guided transcription factor cooperativity shapes face and limb mesenchyme.
Authors: Kim, S. / Morgunova, E. / Naqvi, S. / Goovaerts, S. / Bader, M. / Koska, M. / Popov, A. / Luong, C. / Pogson, A. / Swigut, T. / Claes, P. / Taipale, J. / Wysocka, J.
History
DepositionApr 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation
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_PubMed / _citation.title
Revision 1.2Feb 14, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: DNA (25-MER)
W: DNA (25-MER)
E: Homeobox protein aristaless-like 4
A: Transcription factor 4
B: Twist-related protein 1


Theoretical massNumber of molelcules
Total (without water)38,1605
Polymers38,1605
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-70 kcal/mol
Surface area17740 Å2
Unit cell
Length a, b, c (Å)60.589, 60.589, 237.289
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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DNA chain , 2 types, 2 molecules XW

#1: DNA chain DNA (25-MER)


Mass: 7745.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (25-MER)


Mass: 7606.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein , 3 types, 3 molecules EAB

#3: Protein Homeobox protein aristaless-like 4


Mass: 7809.821 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALX4, KIAA1788 / Plasmid: Rosetta / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H161
#4: Protein Transcription factor 4 / TCF-4 / Class B basic helix-loop-helix protein 19 / bHLHb19 / Immunoglobulin transcription factor 2 ...TCF-4 / Class B basic helix-loop-helix protein 19 / bHLHb19 / Immunoglobulin transcription factor 2 / ITF-2 / SL3-3 enhancer factor 2 / SEF-2


Mass: 7132.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCF4, BHLHB19, ITF2, SEF2 / Plasmid: Rosetta / Production host: Escherichia coli (E. coli) / References: UniProt: P15884
#5: Protein Twist-related protein 1 / Class A basic helix-loop-helix protein 38 / bHLHa38 / H-twist


Mass: 7865.970 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TWIST1, BHLHA38, TWIST / Plasmid: Rosetta / Production host: Escherichia coli (E. coli) / References: UniProt: Q15672

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Non-polymers , 1 types, 27 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sodium Cacodylate buffer (pH 7.5), 100 mM magnesium acetate, 18 % Glycerol, 20 % 2-Methyl-2,4-pentanediol, 6-7% PEG (Mw 8000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.82→47.99 Å / Num. obs: 12686 / % possible obs: 97.9 % / Redundancy: 10.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.068 / Rrim(I) all: 0.223 / Χ2: 0.99 / Net I/σ(I): 8 / Num. measured all: 132310
Reflection shellResolution: 2.82→2.98 Å / % possible obs: 86.4 % / Redundancy: 10.4 % / Rmerge(I) obs: 4.877 / Num. measured all: 16496 / Num. unique obs: 1581 / CC1/2: 0.149 / Rpim(I) all: 1.546 / Rrim(I) all: 5.126 / Χ2: 1.04 / Net I/σ(I) obs: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 19.483 / SU ML: 0.359 / Cross valid method: THROUGHOUT / ESU R: 1.297 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26987 598 5 %RANDOM
Rwork0.21968 ---
obs0.22251 11318 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.448 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.54 Å2-0 Å2
2--1.08 Å2-0 Å2
3----3.5 Å2
Refinement stepCycle: 1 / Resolution: 2.9→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 1025 0 27 2644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122837
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152209
X-RAY DIFFRACTIONr_angle_refined_deg1.9651.6993959
X-RAY DIFFRACTIONr_angle_other_deg1.141.5775087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6425.575453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67119.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.22215330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5971527
X-RAY DIFFRACTIONr_chiral_restr0.1670.232452
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022421
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02610
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.9558.95756
X-RAY DIFFRACTIONr_mcbond_other7.9528.94755
X-RAY DIFFRACTIONr_mcangle_it11.73813.438942
X-RAY DIFFRACTIONr_mcangle_other11.73313.451943
X-RAY DIFFRACTIONr_scbond_it8.5319.1622081
X-RAY DIFFRACTIONr_scbond_other8.5229.1512079
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.04913.6043016
X-RAY DIFFRACTIONr_long_range_B_refined16.6468869
X-RAY DIFFRACTIONr_long_range_B_other16.6438869
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 35 -
Rwork0.451 804 -
obs--99.88 %

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