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- PDB-5no6: TEAD4-HOXB13 complex bound to DNA -

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Basic information

Entry
Database: PDB / ID: 5no6
TitleTEAD4-HOXB13 complex bound to DNA
Components
  • (DNA) x 2
  • Homeobox protein Hox-B13
  • Transcriptional enhancer factor TEF-3
KeywordsTRANSCRIPTION / Transcription factor / DNA binding
Function / homology
Function and homology information


trophectodermal cell fate commitment / epithelial cell maturation involved in prostate gland development / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / Formation of axial mesoderm / methyl-CpG binding / regulation of growth / cell fate specification / muscle organ development ...trophectodermal cell fate commitment / epithelial cell maturation involved in prostate gland development / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / Formation of axial mesoderm / methyl-CpG binding / regulation of growth / cell fate specification / muscle organ development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / positive regulation of stem cell population maintenance / Zygotic genome activation (ZGA) / response to testosterone / epidermis development / embryonic organ development / embryo implantation / skeletal system development / protein-DNA complex / 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 / DNA-binding transcription factor activity / DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Homeobox protein Hox1A3 N-terminal / : / Hox protein A13 N terminal / Transcriptional enhancer factor TEF-3 (TEAD4) / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. / TEA domain profile. ...Homeobox protein Hox1A3 N-terminal / : / Hox protein A13 N terminal / Transcriptional enhancer factor TEF-3 (TEAD4) / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. / TEA domain profile. / TEA domain / YAP binding domain / : / YAP binding 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) / Transcriptional enhancer factor TEF-3 / Homeobox protein Hox-B13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.88 Å
AuthorsMorgunova, E. / Jolma, A. / Yin, Y. / 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
DepositionApr 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 Hox-B13
C: DNA
F: DNA
B: Homeobox protein Hox-B13
D: DNA
E: DNA
I: Transcriptional enhancer factor TEF-3
N: Transcriptional enhancer factor TEF-3


Theoretical massNumber of molelcules
Total (without water)54,1148
Polymers54,1148
Non-polymers00
Water28816
1
A: Homeobox protein Hox-B13
C: DNA
F: DNA
N: Transcriptional enhancer factor TEF-3


Theoretical massNumber of molelcules
Total (without water)27,0574
Polymers27,0574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-26 kcal/mol
Surface area14300 Å2
MethodPISA
2
B: Homeobox protein Hox-B13
D: DNA
E: DNA
I: Transcriptional enhancer factor TEF-3


Theoretical massNumber of molelcules
Total (without water)27,0574
Polymers27,0574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-26 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.659, 56.674, 144.993
Angle α, β, γ (deg.)90.00, 93.81, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Homeobox protein Hox-B13


Mass: 7510.880 Da / Num. of mol.: 2
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
#2: DNA chain DNA


Mass: 5471.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA


Mass: 5556.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Protein Transcriptional enhancer factor TEF-3 / TEA domain family member 4 / TEAD-4 / Transcription factor 13-like 1 / Transcription factor RTEF-1


Mass: 8517.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD4, RTEF1, TCF13L1, TEF3 / Plasmid: pETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q15561
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.24 / Details: PEG (4000), Ammonium sulphate, PME(550, MOPs

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.88→46.71 Å / Num. obs: 14626 / % possible obs: 95.1 % / Redundancy: 2.4 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.029 / Rrim(I) all: 0.049 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.88-3.062.41.8450.2571.3312.28894.8
8.65-46.712.30.01210.0090.01588.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.9data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EEA

5eea


Resolution: 2.88→45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 32.537 / SU ML: 0.569 / Cross valid method: THROUGHOUT / ESU R Free: 0.49 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31677 765 5.2 %RANDOM
Rwork0.23955 ---
obs0.24371 13860 95.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 125.688 Å2
Baniso -1Baniso -2Baniso -3
1-2.99 Å20 Å23.45 Å2
2--1.42 Å20 Å2
3----4.82 Å2
Refinement stepCycle: 1 / Resolution: 2.88→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 1476 0 16 3722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0163984
X-RAY DIFFRACTIONr_bond_other_d0.0030.023170
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.6125547
X-RAY DIFFRACTIONr_angle_other_deg1.30737334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg29.5756.764409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05121.1100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.73215458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8221535
X-RAY DIFFRACTIONr_chiral_restr0.2580.232601
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023289
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02877
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_it8.83613.5731064
X-RAY DIFFRACTIONr_mcbond_other8.82113.5731063
X-RAY DIFFRACTIONr_mcangle_it14.27420.3151323
X-RAY DIFFRACTIONr_mcangle_other14.26820.3151324
X-RAY DIFFRACTIONr_scbond_it7.53612.0342920
X-RAY DIFFRACTIONr_scbond_other7.53212.0332918
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.77617.9294224
X-RAY DIFFRACTIONr_long_range_B_refined16.96812357
X-RAY DIFFRACTIONr_long_range_B_other16.96812358
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.883→2.958 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 53 -
Rwork0.421 1016 -
obs--92.63 %

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