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- PDB-5yya: Crystal structure of Tandem Tudor Domain of human UHRF1 -

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Basic information

Entry
Database: PDB / ID: 5yya
TitleCrystal structure of Tandem Tudor Domain of human UHRF1
ComponentsE3 ubiquitin-protein ligase UHRF1
KeywordsTRANSFERASE / Maintenance of DNA methylation
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly ...histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / mitotic spindle assembly / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / heterochromatin / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / positive regulation of protein metabolic process / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / replication fork / double-strand break repair via homologous recombination / euchromatin / RING-type E3 ubiquitin transferase / nuclear matrix / spindle / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / ubiquitin-dependent protein catabolic process / nucleic acid binding / protein ubiquitination / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / SH3 type barrels. - #30 ...: / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / SH3 type barrels. - #30 / PUA-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKori, S. / Defossez, P.A. / Arita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSTPRESTO 14530337 Japan
CitationJournal: Structure / Year: 2019
Title: Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation.
Authors: Kori, S. / Ferry, L. / Matano, S. / Jimenji, T. / Kodera, N. / Tsusaka, T. / Matsumura, R. / Oda, T. / Sato, M. / Dohmae, N. / Ando, T. / Shinkai, Y. / Defossez, P.A. / Arita, K.
History
DepositionDec 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Nov 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: E3 ubiquitin-protein ligase UHRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4965
Polymers19,2131
Non-polymers2824
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-0 kcal/mol
Surface area10030 Å2
Unit cell
Length a, b, c (Å)38.790, 60.004, 68.903
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 E3 ubiquitin-protein ligase UHRF1 / Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein ...Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein Np95 / hNp95 / RING finger protein 106 / RING-type E3 ubiquitin transferase UHRF1 / Transcription factor ICBP90 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / hUHRF1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 19213.277 Da / Num. of mol.: 1 / Fragment: Tandem Tudor Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: Q96T88, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris (pH 6.5), 200 mM ammonium acetate, 25% (w/v) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→45.25 Å / Num. obs: 17949 / % possible obs: 97.9 % / Redundancy: 6.5 % / Net I/σ(I): 6.5
Reflection shellResolution: 1.7→1.73 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DB3

3db3


Resolution: 1.7→34.452 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.74
RfactorNum. reflection% reflection
Rfree0.2055 886 4.95 %
Rwork0.1719 --
obs0.1736 17884 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 17 244 1574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041378
X-RAY DIFFRACTIONf_angle_d0.6261869
X-RAY DIFFRACTIONf_dihedral_angle_d10.8581156
X-RAY DIFFRACTIONf_chiral_restr0.054195
X-RAY DIFFRACTIONf_plane_restr0.005251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.80650.21381200.19142535X-RAY DIFFRACTION89
1.8065-1.9460.2331360.17762830X-RAY DIFFRACTION99
1.946-2.14180.19891590.16852839X-RAY DIFFRACTION99
2.1418-2.45160.22871510.17672853X-RAY DIFFRACTION100
2.4516-3.08850.24031620.18322891X-RAY DIFFRACTION100
3.0885-34.45860.17291580.16093050X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6701-0.58380.36791.0955-1.37842.3748-0.0476-0.1286-0.02230.1619-0.02520.0067-0.04790.05570.05480.14470.01610.00790.1253-0.01030.1245-8.2064.7707-3.8128
23.3369-0.1383-3.07261.9504-2.07035.30820.1018-0.08170.0889-0.03450.0265-0.1992-0.687-0.0868-0.06710.32680.0869-0.00830.2153-0.01490.1708-14.51314.67517.806
32.91450.4898-1.91121.7058-1.38154.10890.20790.21680.41770.1819-0.01670.1361-0.3531-0.1365-0.00040.19620.0367-0.00440.19230.00080.1914-9.66657.08690.0175
40.9505-0.51370.44081.7687-0.8081.83160.0070.0133-0.0114-0.0015-0.00140.07480.02550.06490.00940.07880.00690.02360.0854-0.00910.1031-13.392712.3466-19.3955
51.3734-0.19710.80681.1516-0.49852.5785-0.04650.24160.0797-0.13770.04550.1075-0.2088-0.12890.01090.12280.011-0.01620.12840.01640.1333-17.865818.2937-28.8978
63.4009-0.81640.99273.0497-1.57193.5048-0.0353-0.1980.41960.41250.0190.036-0.6573-0.24640.05820.17660.01240.01050.106-0.00660.1554-16.082524.1159-19.7539
71.42670.7522-1.54122.4878-2.81894.4890.03480.1751-0.04320.00210.0120.15450.1802-0.1101-0.05660.1182-0.00430.0110.1003-0.02630.1466-16.55417.9185-21.716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 126 through 160 )
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 170 )
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 195 )
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 236 )
5X-RAY DIFFRACTION5chain 'A' and (resid 237 through 259 )
6X-RAY DIFFRACTION6chain 'A' and (resid 260 through 271 )
7X-RAY DIFFRACTION7chain 'A' and (resid 272 through 285 )

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