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- PDB-7t7t: Structure of TSK/BRU1 bound to histone H3.1 -

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Basic information

Entry
Database: PDB / ID: 7t7t
TitleStructure of TSK/BRU1 bound to histone H3.1
Components
  • Histone H3.1
  • Protein TONSOKU
KeywordsNUCLEAR PROTEIN / Epigenetic protein / H3.1 reader / nucleosome
Function / homology
Function and homology information


meristem structural organization / response to DNA damage checkpoint signaling / chromocenter / plastid / epigenetic regulation of gene expression / structural constituent of chromatin / nucleosome / chromosome / histone binding / protein heterodimerization activity ...meristem structural organization / response to DNA damage checkpoint signaling / chromocenter / plastid / epigenetic regulation of gene expression / structural constituent of chromatin / nucleosome / chromosome / histone binding / protein heterodimerization activity / DNA repair / DNA binding / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Protein TONSOKU / Leucine rich repeat, ribonuclease inhibitor type / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Leucine-rich repeat domain superfamily / Histone H3 signature 1. ...Protein TONSOKU / Leucine rich repeat, ribonuclease inhibitor type / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Leucine-rich repeat domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Protein TONSOKU / Histone H3.1
Similarity search - Component
Biological speciesCitrus unshiu (satsuma mandarin)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.17 Å
AuthorsDavarinejad, H. / Couture, J.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Science / Year: 2022
Title: The histone H3.1 variant regulates TONSOKU-mediated DNA repair during replication.
Authors: Davarinejad, H. / Huang, Y.C. / Mermaz, B. / LeBlanc, C. / Poulet, A. / Thomson, G. / Joly, V. / Munoz, M. / Arvanitis-Vigneault, A. / Valsakumar, D. / Villarino, G. / Ross, A. / Rotstein, B. ...Authors: Davarinejad, H. / Huang, Y.C. / Mermaz, B. / LeBlanc, C. / Poulet, A. / Thomson, G. / Joly, V. / Munoz, M. / Arvanitis-Vigneault, A. / Valsakumar, D. / Villarino, G. / Ross, A. / Rotstein, B.H. / Alarcon, E.I. / Brunzelle, J.S. / Voigt, P. / Dong, J. / Couture, J.F. / Jacob, Y.
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein TONSOKU
B: Protein TONSOKU
X: Histone H3.1
W: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)134,8634
Polymers134,8634
Non-polymers00
Water181
1
A: Protein TONSOKU
W: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)67,4322
Polymers67,4322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-14 kcal/mol
Surface area22520 Å2
MethodPISA
2
B: Protein TONSOKU
X: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)67,4322
Polymers67,4322
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-16 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.890, 92.330, 209.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 2 through 7 and (name N...
d_2ens_1(chain "B" and ((resid 2 through 7 and (name N...
d_1ens_2(chain "W" and (resid 4 or (resid 5 through 18...
d_2ens_2(chain "X" and resid 4 through 36)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYASPA2 - 56
d_12ens_1LEUSERA67 - 102
d_13ens_1VALPHEA105 - 122
d_14ens_1TYRTHRA125 - 143
d_15ens_1PHEILEA148 - 306
d_16ens_1GLYILEA310 - 395
d_17ens_1GLUALAA399 - 419
d_18ens_1LEUASPA422 - 423
d_19ens_1PROGLNA438 - 466
d_21ens_1GLYPHEB1 - 109
d_22ens_1TYRGLUB112 - 148
d_23ens_1ASPGLUB150 - 169
d_24ens_1ASPGLNB174 - 432
d_11ens_2LYSLYSD1 - 24
d_21ens_2LYSLYSC2 - 25

NCS ensembles :
ID
ens_1
ens_2

NCS oper: (Code: givenMatrix: (0.285457550751, 0.958362648068, -0.00741764842175), (-0.956606169973, 0.284445120165, -0.0632108312277), (-0.0584689857053, 0.0251397773101, 0.997972629538)Vector: -14. ...NCS oper: (Code: given
Matrix: (0.285457550751, 0.958362648068, -0.00741764842175), (-0.956606169973, 0.284445120165, -0.0632108312277), (-0.0584689857053, 0.0251397773101, 0.997972629538)
Vector: -14.5493573448, -19.248230852, -53.1442852977)

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Components

#1: Protein Protein TONSOKU


Mass: 62659.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus unshiu (satsuma mandarin) / Gene: CUMW_187040 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2H5Q1B8
#2: Protein/peptide Histone H3.1 / Histone H3.2


Mass: 4771.602 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% 1,2-Propanediol, 20% glycerol, 0.1M sodium potassium phosphate pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.17→38.53 Å / Num. obs: 28135 / % possible obs: 99.9 % / Redundancy: 26.1 % / Biso Wilson estimate: 31.7 Å2 / CC1/2: 0.99 / Net I/σ(I): 19.5
Reflection shellResolution: 3.17→3.25 Å / Num. unique obs: 2036 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
SHELXDEphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIX1.19.2_4158refinement
Coot0.9.4model building
RefinementMethod to determine structure: SAD / Resolution: 3.17→38.53 Å / SU ML: 0.4629 / Cross valid method: FREE R-VALUE / σ(F): 0.39 / Phase error: 31.3428
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3183 2000 7.31 %
Rwork0.2787 25366 -
obs0.2816 27366 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.29 Å2
Refinement stepCycle: LAST / Resolution: 3.17→38.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7175 0 0 1 7176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00357268
X-RAY DIFFRACTIONf_angle_d0.73529786
X-RAY DIFFRACTIONf_chiral_restr0.04271097
X-RAY DIFFRACTIONf_plane_restr0.00671264
X-RAY DIFFRACTIONf_dihedral_angle_d4.98731010
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.01006264411
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS2.71288391924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.250.38161300.3621647X-RAY DIFFRACTION90.76
3.25-3.340.37731330.33211695X-RAY DIFFRACTION92.51
3.34-3.440.37881370.3211725X-RAY DIFFRACTION93.95
3.44-3.550.35251380.3051756X-RAY DIFFRACTION96.24
3.55-3.670.31041390.29071759X-RAY DIFFRACTION95.96
3.67-3.820.34341410.27241803X-RAY DIFFRACTION97.89
3.82-3.990.33581430.2731809X-RAY DIFFRACTION98.64
3.99-4.20.31451450.26531836X-RAY DIFFRACTION99.15
4.2-4.470.26921440.22391824X-RAY DIFFRACTION99.44
4.47-4.810.23291460.23771863X-RAY DIFFRACTION99.75
4.81-5.290.32361470.26431862X-RAY DIFFRACTION99.95
5.29-6.060.35491480.29721879X-RAY DIFFRACTION99.85
6.06-7.620.30721510.27621914X-RAY DIFFRACTION100
7.62-38.530.27531580.25711994X-RAY DIFFRACTION99.68

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