[English] 日本語
Yorodumi
- PDB-5yy9: Crystal structure of Tandem Tudor Domain of human UHRF1 in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yy9
TitleCrystal structure of Tandem Tudor Domain of human UHRF1 in complex with LIG1-K126me3
Components
  • E3 ubiquitin-protein ligase UHRF1
  • Ligase 1
KeywordsTRANSFERASE / Maintenance of DNA methylation
Function / homology
Function and homology information


Okazaki fragment processing involved in mitotic DNA replication / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / histone H3 ubiquitin ligase activity / DNA ligase activity / DNA damage sensor activity / DNA ligase (ATP) / DNA ligase (ATP) activity / hemi-methylated DNA-binding / histone H3K9me2/3 reader activity / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence ...Okazaki fragment processing involved in mitotic DNA replication / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / histone H3 ubiquitin ligase activity / DNA ligase activity / DNA damage sensor activity / DNA ligase (ATP) / DNA ligase (ATP) activity / hemi-methylated DNA-binding / histone H3K9me2/3 reader activity / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / homologous recombination / Processive synthesis on the lagging strand / regulation of epithelial cell proliferation / lagging strand elongation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / DNA biosynthetic process / Early Phase of HIV Life Cycle / positive regulation of protein metabolic process / POLB-Dependent Long Patch Base Excision Repair / anatomical structure morphogenesis / mitotic spindle assembly / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / heterochromatin / cis-regulatory region sequence-specific DNA binding / protein autoubiquitination / base-excision repair, gap-filling / : / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / epigenetic regulation of gene expression / replication fork / Gap-filling DNA repair synthesis and ligation in GG-NER / double-strand break repair via homologous recombination / euchromatin / RING-type E3 ubiquitin transferase / base-excision repair / spindle / nuclear matrix / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / heterochromatin formation / ubiquitin-dependent protein catabolic process / DNA recombination / histone binding / nucleic acid binding / protein ubiquitination / cell division / DNA repair / intracellular membrane-bounded organelle / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus
Similarity search - Function
: / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / 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. ...: / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / 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. / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / SH3 type barrels. - #30 / PUA-like superfamily / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-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 / Nucleic acid-binding, OB-fold / Mainly Beta
Similarity search - Domain/homology
DNA ligase 1 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.653 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UHRF1
B: E3 ubiquitin-protein ligase UHRF1
C: Ligase 1
D: Ligase 1


Theoretical massNumber of molelcules
Total (without water)39,6054
Polymers39,6054
Non-polymers00
Water43224
1
A: E3 ubiquitin-protein ligase UHRF1
C: Ligase 1


Theoretical massNumber of molelcules
Total (without water)19,8022
Polymers19,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-4 kcal/mol
Surface area9240 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UHRF1
D: Ligase 1


Theoretical massNumber of molelcules
Total (without water)19,8022
Polymers19,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-5 kcal/mol
Surface area8780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.105, 97.349, 132.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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: 18162.207 Da / Num. of mol.: 2 / 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: Protein/peptide Ligase 1


Mass: 1640.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P18858*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 00 mM Tris-HCl (pH 7.0), 200 mM tri-potassium phosphate and 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→48.67 Å / Num. obs: 40019 / % possible obs: 97 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.5
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.95 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DB3

3db3


Resolution: 2.653→40.228 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.67
RfactorNum. reflection% reflection
Rfree0.2877 1034 9.97 %
Rwork0.2309 --
obs0.2367 10370 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.653→40.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 0 24 2414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042435
X-RAY DIFFRACTIONf_angle_d0.8123304
X-RAY DIFFRACTIONf_dihedral_angle_d21.6511464
X-RAY DIFFRACTIONf_chiral_restr0.053360
X-RAY DIFFRACTIONf_plane_restr0.006429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6535-2.79340.38011340.30681269X-RAY DIFFRACTION94
2.7934-2.96830.39261560.29991327X-RAY DIFFRACTION98
2.9683-3.19740.33441480.2771315X-RAY DIFFRACTION98
3.1974-3.5190.28781430.24231330X-RAY DIFFRACTION96
3.519-4.02780.23991620.22171334X-RAY DIFFRACTION97
4.0278-5.0730.2431330.17761344X-RAY DIFFRACTION95
5.073-40.23260.30011580.22331417X-RAY DIFFRACTION94

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more