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- PDB-4d6k: Structure of DNTTIP1 dimerisation domain. -

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Basic information

Entry
Database: PDB / ID: 4d6k
TitleStructure of DNTTIP1 dimerisation domain.
ComponentsDEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1
KeywordsTRANSCRIPTION / HDAC1 / MIDEAS / HISTONE DEACETYLASE COMPLEX / TDIF1
Function / homology
Function and homology information


histone deacetylase complex / nucleosome binding / chromosome / nucleolus / protein homodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Terminal deoxynucleotidyltransferase-interacting factor 1 / DNTTIP1, dimerisation domain / : / DNTTIP1 dimerisation domain / TdIF1, C-terminal
Similarity search - Domain/homology
Deoxynucleotidyltransferase terminal-interacting protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsItoh, T. / Fairall, L. / Schwabe, J.W.R.
CitationJournal: Nucleic Acids Res / Year: 2015
Title: Structural and functional characterization of a cell cycle associated HDAC1/2 complex reveals the structural basis for complex assembly and nucleosome targeting.
Authors: Toshimasa Itoh / Louise Fairall / Frederick W Muskett / Charles P Milano / Peter J Watson / Nadia Arnaudo / Almutasem Saleh / Christopher J Millard / Mohammed El-Mezgueldi / Fabrizio Martino ...Authors: Toshimasa Itoh / Louise Fairall / Frederick W Muskett / Charles P Milano / Peter J Watson / Nadia Arnaudo / Almutasem Saleh / Christopher J Millard / Mohammed El-Mezgueldi / Fabrizio Martino / John W R Schwabe /
Abstract: Recent proteomic studies have identified a novel histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. This complex is conserved from nematodes to man and ...Recent proteomic studies have identified a novel histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. This complex is conserved from nematodes to man and contains histone deacetylases 1 and 2, the MIDEAS corepressor protein and a protein called DNTTIP1 whose function was hitherto poorly understood. Here, we report the structures of two domains from DNTTIP1. The amino-terminal region forms a tight dimerization domain with a novel structural fold that interacts with and mediates assembly of the HDAC1:MIDEAS complex. The carboxy-terminal domain of DNTTIP1 has a structure related to the SKI/SNO/DAC domain, despite lacking obvious sequence homology. We show that this domain in DNTTIP1 mediates interaction with both DNA and nucleosomes. Thus, DNTTIP1 acts as a dimeric chromatin binding module in the HDAC1:MIDEAS corepressor complex.
History
DepositionNov 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns_shell
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1
B: DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1
C: DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1
D: DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1
E: DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1
F: DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)62,5506
Polymers62,5506
Non-polymers00
Water2,324129
1
A: DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1
B: DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)20,8502
Polymers20,8502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-44.9 kcal/mol
Surface area8340 Å2
MethodPISA
2
E: DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1
F: DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)20,8502
Polymers20,8502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-40.5 kcal/mol
Surface area7630 Å2
MethodPISA
3
C: DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1
D: DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)20,8502
Polymers20,8502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-40.2 kcal/mol
Surface area8120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.910, 103.051, 108.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DEOXYNUCLEOTIDYLTRANSFERASE TERMINAL-INTERACTING PROTEIN 1 / TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE-INTERACTING FACTOR 1 / TDIF1 / TDT-INTERACTING FACTOR 1 / DNTTIP1


Mass: 10424.954 Da / Num. of mol.: 6 / Fragment: DIMERISATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q9H147
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.47 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.6 / Details: 100 MM SODIUM ACETATE PH 4.6 14% PROPAN-2-OL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→74.87 Å / Num. obs: 34537 / % possible obs: 98.9 % / Observed criterion σ(I): 3.4 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.4 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.1→74.95 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.712 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22448 1818 5 %RANDOM
Rwork0.19541 ---
obs0.19687 34537 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.106 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--1.86 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→74.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 0 129 3441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193421
X-RAY DIFFRACTIONr_bond_other_d0.010.023350
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.9744616
X-RAY DIFFRACTIONr_angle_other_deg1.7337717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4265432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23325.876177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77915660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6171521
X-RAY DIFFRACTIONr_chiral_restr0.1030.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023931
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02766
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_it3.3433.3161692
X-RAY DIFFRACTIONr_mcbond_other3.3323.3151691
X-RAY DIFFRACTIONr_mcangle_it4.7334.922112
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6133.8111729
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 101 -
Rwork0.234 2285 -
obs--90.11 %

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