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- PDB-7ebk: Mouse Trim66 PHD-Bromo dual domain complexed with the H3(1-24)K9m... -

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Basic information

Entry
Database: PDB / ID: 7ebk
TitleMouse Trim66 PHD-Bromo dual domain complexed with the H3(1-24)K9me3K18ac peptide
Components
  • H3K9me3K18ac
  • Tripartite motif-containing protein 66
KeywordsGENE REGULATION / histone modification / PHD finger / Bromodomain / epigenetics
Function / homology
Function and homology information


zinc ion binding / nucleus
Similarity search - Function
Tripartite motif-containing protein 66 / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. ...Tripartite motif-containing protein 66 / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Tripartite motif-containing protein 66
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsWang, Z. / Jiang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071204 China
Citation
Journal: Cell Stem Cell / Year: 2022
Title: A TRIM66/DAX1/Dux axis suppresses the totipotent 2-cell-like state in murine embryonic stem cells.
Authors: Zuo, F. / Jiang, J. / Fu, H. / Yan, K. / Liefke, R. / Zhang, J. / Hong, Y. / Chang, Z. / Liu, N. / Wang, Z. / Xi, Q.
#1: Journal: To Be Published
Title: Structure of the Trim66 PHD-Bromo dual domain complexed with histone H3 peptide containing trimethylated K9 and acetylated K18
Authors: Jiang, J. / Wang, Z.
History
DepositionMar 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tripartite motif-containing protein 66
B: H3K9me3K18ac
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3034
Polymers24,1722
Non-polymers1312
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-7 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.646, 64.646, 251.744
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Tripartite motif-containing protein 66


Mass: 21525.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trim66 / Production host: Escherichia coli (E. coli) / References: UniProt: E9PZP2
#2: Protein/peptide H3K9me3K18ac


Mass: 2646.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.39 Å3/Da / Density % sol: 63.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 15% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.0, 2% w/v Polyethylene glycol 3350
PH range: 7

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 32908 / % possible obs: 98.9 % / Redundancy: 25.7 % / Biso Wilson estimate: 30.16 Å2 / Rsym value: 0.076 / Net I/σ(I): 61.3
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 1568 / Rsym value: 0.958

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O33

3o33


Resolution: 1.74→41.83 Å / SU ML: 0.183 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2284 1667 5.07 %
Rwork0.2134 31198 -
obs0.2142 32865 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.31 Å2
Refinement stepCycle: LAST / Resolution: 1.74→41.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1560 0 2 188 1750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711598
X-RAY DIFFRACTIONf_angle_d0.8852161
X-RAY DIFFRACTIONf_chiral_restr0.0518230
X-RAY DIFFRACTIONf_plane_restr0.007277
X-RAY DIFFRACTIONf_dihedral_angle_d14.652605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.790.29191260.25482450X-RAY DIFFRACTION95.9
1.79-1.850.32111380.28732518X-RAY DIFFRACTION98.41
1.85-1.910.32251470.29242513X-RAY DIFFRACTION98.56
1.91-1.990.26011370.24832532X-RAY DIFFRACTION98.74
1.99-2.080.23471400.23942565X-RAY DIFFRACTION98.9
2.08-2.190.28851310.22922542X-RAY DIFFRACTION99.07
2.19-2.330.27871420.23982582X-RAY DIFFRACTION99.2
2.33-2.510.23631380.2262588X-RAY DIFFRACTION99.16
2.51-2.760.26191360.22512623X-RAY DIFFRACTION99.6
2.76-3.160.22671430.21652644X-RAY DIFFRACTION99.82
3.16-3.980.20791260.19542730X-RAY DIFFRACTION99.9
3.98-41.830.18581630.18862911X-RAY DIFFRACTION99.84

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