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- PDB-5edn: Structure of HOXB13-DNA(TCG) complex -

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Basic information

Entry
Database: PDB / ID: 5edn
TitleStructure of HOXB13-DNA(TCG) complex
Components
  • DNA (5'-D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
  • Homeobox protein Hox-B13
KeywordsTRANSCRIPTION / transcription factor / DNA / complex
Function / homology
Function and homology information


epithelial cell maturation involved in prostate gland development / methyl-CpG binding / regulation of growth / response to testosterone / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epidermis development / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / sequence-specific double-stranded DNA binding / angiogenesis ...epithelial cell maturation involved in prostate gland development / methyl-CpG binding / regulation of growth / response to testosterone / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epidermis development / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / sequence-specific double-stranded DNA binding / 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 / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
Homeobox protein Hox1A3 N-terminal / Hox protein A13 N terminal / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily ...Homeobox protein Hox1A3 N-terminal / Hox protein A13 N terminal / 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 Hox-B13
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMorgunova, E. / Yin, Y. / Jolma, A. / Popov, A. / Taipale, J.
CitationJournal: Elife / Year: 2018
Title: Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.
Authors: Morgunova, E. / Yin, Y. / Das, P.K. / Jolma, A. / Zhu, F. / Popov, A. / Xu, Y. / Nilsson, L. / Taipale, J.
History
DepositionOct 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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
A: Homeobox protein Hox-B13
B: Homeobox protein Hox-B13
C: DNA (5'-D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
D: DNA (5'-D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
E: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3')
F: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3')
G: Homeobox protein Hox-B13
H: DNA (5'-D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
I: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3')
J: Homeobox protein Hox-B13
K: DNA (5'-D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
L: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,67913
Polymers82,55612
Non-polymers1221
Water30617
1
A: Homeobox protein Hox-B13
C: DNA (5'-D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
F: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7614
Polymers20,6393
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-9 kcal/mol
Surface area10170 Å2
MethodPISA
2
B: Homeobox protein Hox-B13
D: DNA (5'-D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
E: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)20,6393
Polymers20,6393
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-18 kcal/mol
Surface area10490 Å2
MethodPISA
3
G: Homeobox protein Hox-B13
H: DNA (5'-D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
I: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)20,6393
Polymers20,6393
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-19 kcal/mol
Surface area10400 Å2
MethodPISA
4
J: Homeobox protein Hox-B13
K: DNA (5'-D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')
L: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)20,6393
Polymers20,6393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-24 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.618, 52.522, 389.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein
Homeobox protein Hox-B13 /


Mass: 8989.539 Da / Num. of mol.: 4 / Fragment: UNP residues 209-284
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 (5'-D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3')


Mass: 5857.779 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (5'-D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3')


Mass: 5791.791 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.55 Å3/Da / Density % sol: 65.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 3350, potassium chloride, magnesium chloride, PEG 400, Tris
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: silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.613
11K, H, -L20.387
ReflectionResolution: 3.2→46.29 Å / Num. obs: 17652 / % possible obs: 93.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.7
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 1.9 / % possible all: 81.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XRM

4xrm


Resolution: 3.2→46.29 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 19.626 / SU ML: 0.355 / Cross valid method: THROUGHOUT / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2813 916 5.2 %RANDOM
Rwork0.21617 ---
obs0.21934 16610 92.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 120.992 Å2
Baniso -1Baniso -2Baniso -3
1--93.34 Å20 Å20 Å2
2--74.62 Å20 Å2
3---18.72 Å2
Refinement stepCycle: 1 / Resolution: 3.2→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 3116 8 17 5197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0145572
X-RAY DIFFRACTIONr_bond_other_d0.0040.023928
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.458116
X-RAY DIFFRACTIONr_angle_other_deg1.50639143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2955238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87420.90999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.61815473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8861535
X-RAY DIFFRACTIONr_chiral_restr0.1330.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024041
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021262
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_it10.52611.683965
X-RAY DIFFRACTIONr_mcbond_other10.53411.684963
X-RAY DIFFRACTIONr_mcangle_it16.30517.5211198
X-RAY DIFFRACTIONr_mcangle_other16.29817.5241199
X-RAY DIFFRACTIONr_scbond_it10.11712.6364607
X-RAY DIFFRACTIONr_scbond_other10.11712.6364607
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.81218.8476919
X-RAY DIFFRACTIONr_long_range_B_refined22.76210193
X-RAY DIFFRACTIONr_long_range_B_other22.76110194
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.196→3.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 41 -
Rwork0.301 873 -
obs--64.78 %

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