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- PDB-5ef6: Structure of HOXB13 complex with methylated DNA -

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Basic information

Entry
Database: PDB / ID: 5ef6
TitleStructure of HOXB13 complex with methylated DNA
Components
  • DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*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*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3')
  • Homeobox protein Hox-B13
KeywordsTRANSCRIPTION / transcription factor / methylated 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: 3 Å
AuthorsMorgunova, E. / Yin, Y. / Jolma, A. / Popov, A. / Taipale, J.
CitationJournal: Science / Year: 2017
Title: Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Authors: Yin, Y. / Morgunova, E. / Jolma, A. / Kaasinen, E. / Sahu, B. / Khund-Sayeed, S. / Das, P.K. / Kivioja, T. / Dave, K. / Zhong, F. / Nitta, K.R. / Taipale, M. / Popov, A. / Ginno, P.A. / ...Authors: Yin, Y. / Morgunova, E. / Jolma, A. / Kaasinen, E. / Sahu, B. / Khund-Sayeed, S. / Das, P.K. / Kivioja, T. / Dave, K. / Zhong, F. / Nitta, K.R. / Taipale, M. / Popov, A. / Ginno, P.A. / Domcke, S. / Yan, J. / Schubeler, D. / Vinson, C. / Taipale, J.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
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
C: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3')
F: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
B: Homeobox protein Hox-B13
D: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3')
E: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
G: Homeobox protein Hox-B13
H: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3')
I: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
J: Homeobox protein Hox-B13
K: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3')
L: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)74,28012
Polymers74,28012
Non-polymers00
Water1,820101
1
A: Homeobox protein Hox-B13
C: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3')
F: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)18,5703
Polymers18,5703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-12 kcal/mol
Surface area9540 Å2
MethodPISA
2
B: Homeobox protein Hox-B13
D: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3')
E: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)18,5703
Polymers18,5703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-11 kcal/mol
Surface area9860 Å2
MethodPISA
3
G: Homeobox protein Hox-B13
H: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3')
I: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)18,5703
Polymers18,5703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-12 kcal/mol
Surface area9800 Å2
MethodPISA
4
J: Homeobox protein Hox-B13
K: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3')
L: DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)18,5703
Polymers18,5703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-14 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.969, 55.557, 102.010
Angle α, β, γ (deg.)90.000, 102.240, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Homeobox protein Hox-B13


Mass: 7510.880 Da / Num. of mol.: 4 / Fragment: UNP residues 217-278
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*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*GP*GP*TP*CP*C)-3')


Mass: 5542.600 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*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')


Mass: 5516.636 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 3350, potassium chloride, magnesium chloride, 2-methyl-1-propanol, Tris
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: May 26, 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: 2.98→55.16 Å / Num. all: 17811 / Num. obs: 17019 / % possible obs: 97.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 36.6 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.13 / Rrim(I) all: 0.241 / Net I/σ(I): 5 / Num. measured all: 57890
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.98-3.163.40.864930327480.7810.5491.0261.496.4
8.94-55.1630.04120546850.9990.0280.0513.396.3

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Processing

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

5edn


Resolution: 3→38.169 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 40.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.32 1648 5.18 %random
Rwork0.2907 30142 --
obs0.2923 31790 94.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.57 Å2 / Biso mean: 41.4815 Å2 / Biso min: 4.41 Å2
Refinement stepCycle: final / Resolution: 3→38.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 2960 0 101 5159
Biso mean---26.79 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055434
X-RAY DIFFRACTIONf_angle_d0.9947904
X-RAY DIFFRACTIONf_chiral_restr0.042868
X-RAY DIFFRACTIONf_plane_restr0.003490
X-RAY DIFFRACTIONf_dihedral_angle_d29.872256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.08820.39981570.4112534269195
3.0882-3.18790.5211270.36072466259395
3.1879-3.30180.38181370.3192467260492
3.3018-3.43390.29081360.30482391252792
3.4339-3.590.31751310.29982543267496
3.59-3.77920.32191500.30852501265195
3.7792-4.01570.29711190.27292561268096
4.0157-4.32540.27031120.26582579269196
4.3254-4.75990.31081280.25842510263895
4.7599-5.4470.28631590.26452583274298
5.447-6.85610.32351470.28472543269096
6.8561-38.17240.28091450.25672464260994

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