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- PDB-5eea: Structure of HOXB13-DNA(CAA) complex -

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Basic information

Entry
Database: PDB / ID: 5eea
TitleStructure of HOXB13-DNA(CAA) complex
Components
  • DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / response to testosterone / epidermis development / response to wounding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / angiogenesis ...epithelial cell maturation involved in prostate gland development / methyl-CpG binding / regulation of growth / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / response to testosterone / epidermis development / response to wounding / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / regulation of transcription by RNA polymerase II / chromatin / 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 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: 2.195 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 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 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 1.2Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
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
D: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3')
E: DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
C: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3')
F: DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
H: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3')
I: DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
K: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3')
L: DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
B: Homeobox protein Hox-B13
A: Homeobox protein Hox-B13
G: Homeobox protein Hox-B13
J: Homeobox protein Hox-B13


Theoretical massNumber of molelcules
Total (without water)74,68112
Polymers74,68112
Non-polymers00
Water9,332518
1
D: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3')
E: DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
B: Homeobox protein Hox-B13


Theoretical massNumber of molelcules
Total (without water)18,6703
Polymers18,6703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-24 kcal/mol
Surface area9970 Å2
MethodPISA
2
C: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3')
F: DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
A: Homeobox protein Hox-B13


Theoretical massNumber of molelcules
Total (without water)18,6703
Polymers18,6703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-24 kcal/mol
Surface area9980 Å2
MethodPISA
3
H: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3')
I: DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
G: Homeobox protein Hox-B13


Theoretical massNumber of molelcules
Total (without water)18,6703
Polymers18,6703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-23 kcal/mol
Surface area9970 Å2
MethodPISA
4
K: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3')
L: DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
J: Homeobox protein Hox-B13


Theoretical massNumber of molelcules
Total (without water)18,6703
Polymers18,6703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-25 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.356, 57.918, 101.278
Angle α, β, γ (deg.)90.00, 101.57, 90.00
Int Tables number3
Space group name H-MP121

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Components

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


Mass: 5534.570 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain
DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Mass: 5495.624 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein
Homeobox protein Hox-B13


Mass: 7640.061 Da / Num. of mol.: 4
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 5000, potassium chloride, magnesium chloride, PEG 400
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2015
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.19→46.02 Å / Num. obs: 44173 / % possible obs: 97.5 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 5.9
Reflection shellResolution: 2.19→2.31 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.135 / Mean I/σ(I) obs: 1.2 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5edn

5edn


Resolution: 2.195→45.945 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2965 2458 2.88 %random
Rwork0.2508 ---
obs0.2521 85430 96.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.195→45.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 2949 0 518 5570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115451
X-RAY DIFFRACTIONf_angle_d1.2647925
X-RAY DIFFRACTIONf_dihedral_angle_d28.4662320
X-RAY DIFFRACTIONf_chiral_restr0.076879
X-RAY DIFFRACTIONf_plane_restr0.007496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.195-2.23720.3641870.39433770X-RAY DIFFRACTION78
2.2372-2.28290.35541600.34874666X-RAY DIFFRACTION99
2.2829-2.33250.46821440.34444572X-RAY DIFFRACTION97
2.3325-2.38670.3161250.31184664X-RAY DIFFRACTION98
2.3867-2.44640.35171320.30244629X-RAY DIFFRACTION98
2.4464-2.51260.38861540.29714653X-RAY DIFFRACTION97
2.5126-2.58650.33661300.29334710X-RAY DIFFRACTION99
2.5865-2.670.3021350.27884673X-RAY DIFFRACTION98
2.67-2.76540.38211360.30084658X-RAY DIFFRACTION98
2.7654-2.87610.42581410.30014679X-RAY DIFFRACTION99
2.8761-3.0070.37711400.27224688X-RAY DIFFRACTION98
3.007-3.16550.32561680.26254610X-RAY DIFFRACTION98
3.1655-3.36370.27581400.2334562X-RAY DIFFRACTION96
3.3637-3.62340.27131260.214635X-RAY DIFFRACTION97
3.6234-3.98780.25681350.22174698X-RAY DIFFRACTION99
3.9878-4.56440.24351290.21964731X-RAY DIFFRACTION99
4.5644-5.74890.22151390.20724743X-RAY DIFFRACTION100
5.7489-45.95510.24761370.20954631X-RAY DIFFRACTION97

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