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- PDB-6ieu: The structure of TRIM66 PHD-Bromo domain with unmodified H3 N ter... -

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Basic information

Entry
Database: PDB / ID: 6ieu
TitleThe structure of TRIM66 PHD-Bromo domain with unmodified H3 N terminal peptide
Components
  • ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-LYS-SER-THR-GLY
  • Tripartite motif-containing protein 66
KeywordsTRANSCRIPTION / TRIM66 / PHD-Bromo / H3
Function / homology
Function and homology information


Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) ...Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
Tripartite motif-containing protein 66 / Trim66, B-box zinc-binding domain / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...Tripartite motif-containing protein 66 / Trim66, B-box zinc-binding domain / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / 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 / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tripartite motif-containing protein 66 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.787 Å
AuthorsChen, J.
CitationJournal: Nat Commun / Year: 2019
Title: TRIM66 reads unmodified H3R2K4 and H3K56ac to respond to DNA damage in embryonic stem cells.
Authors: Chen, J. / Wang, Z. / Guo, X. / Li, F. / Wei, Q. / Chen, X. / Gong, D. / Xu, Y. / Chen, W. / Liu, Y. / Kang, J. / Shi, Y.
History
DepositionSep 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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: Tripartite motif-containing protein 66
C: ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-LYS-SER-THR-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2316
Polymers23,9162
Non-polymers3154
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-5 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.266, 63.465, 33.303
Angle α, β, γ (deg.)90.000, 101.670, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tripartite motif-containing protein 66


Mass: 22607.797 Da / Num. of mol.: 1 / Fragment: UNP residues 968-1160
Mutation: L1002T, C1026S, C1030S, H1031Y, M1036K, I1089T, C1135S, V1138N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM66 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15016
#2: Protein/peptide ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-LYS-SER-THR-GLY


Mass: 1308.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES sodium, pH 7.5,10% v/v 2-propanol, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.787→32.614 Å / Num. obs: 19103 / % possible obs: 98.25 % / Redundancy: 4.2 % / Biso Wilson estimate: 30.57 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 22.409
Reflection shellResolution: 1.787→1.851 Å / Rmerge(I) obs: 0.64 / Num. unique obs: 1684

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O33

3o33


Resolution: 1.787→32.614 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 24.19
RfactorNum. reflection% reflection
Rfree0.2165 926 4.85 %
Rwork0.1862 --
obs0.1877 19103 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.02 Å2 / Biso mean: 36.1521 Å2 / Biso min: 19.81 Å2
Refinement stepCycle: final / Resolution: 1.787→32.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 14 106 1547
Biso mean--40.95 39.86 -
Num. residues----180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061474
X-RAY DIFFRACTIONf_angle_d0.8861987
X-RAY DIFFRACTIONf_chiral_restr0.049212
X-RAY DIFFRACTIONf_plane_restr0.007252
X-RAY DIFFRACTIONf_dihedral_angle_d6.984897
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7874-1.88160.29491160.24122364248090
1.8816-1.99950.25031190.212926302749100
1.9995-2.15380.23941310.196526442775100
2.1538-2.37050.23341510.186326062757100
2.3705-2.71340.21651470.196726102757100
2.7134-3.4180.22251380.198526352773100
3.418-32.61950.19331240.16832688281299

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