[English] 日本語
Yorodumi
- PDB-4pw7: structure of UHRF2-SRA in complex with a 5mC-containing DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pw7
Titlestructure of UHRF2-SRA in complex with a 5mC-containing DNA
Components
  • 5mC-containing DNA1
  • 5mC-containing DNA2
  • E3 ubiquitin-protein ligase UHRF2
KeywordsLIGASE/DNA / SRA / 5hmC binding / 5hmC-containing DNA / methylation / nuclear / LIGASE-DNA complex
Function / homology
Function and homology information


histone H3K9me2/3 reader activity / SUMO transferase activity / negative regulation of gene expression via chromosomal CpG island methylation / protein sumoylation / pericentric heterochromatin / heterochromatin / protein autoubiquitination / SUMOylation of transcription cofactors / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity ...histone H3K9me2/3 reader activity / SUMO transferase activity / negative regulation of gene expression via chromosomal CpG island methylation / protein sumoylation / pericentric heterochromatin / heterochromatin / protein autoubiquitination / SUMOylation of transcription cofactors / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / regulation of cell cycle / protein ubiquitination / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / : / SRA-YDG / PUA domain-like / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG ...: / : / : / : / SRA-YDG / PUA domain-like / 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. / 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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Roll / Ubiquitin-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / E3 ubiquitin-protein ligase UHRF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsZHou, T. / Xiong, J. / Wang, M. / Yang, N. / Wong, J. / Zhu, B. / Xu, R.M.
CitationJournal: Mol.Cell / Year: 2014
Title: Structural Basis for Hydroxymethylcytosine Recognition by the SRA Domain of UHRF2.
Authors: Zhou, T. / Xiong, J. / Wang, M. / Yang, N. / Wong, J. / Zhu, B. / Xu, R.M.
History
DepositionMar 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase UHRF2
B: E3 ubiquitin-protein ligase UHRF2
C: 5mC-containing DNA1
D: 5mC-containing DNA2
E: E3 ubiquitin-protein ligase UHRF2
F: E3 ubiquitin-protein ligase UHRF2
G: 5mC-containing DNA1
H: 5mC-containing DNA2


Theoretical massNumber of molelcules
Total (without water)116,9218
Polymers116,9218
Non-polymers00
Water16,790932
1
A: E3 ubiquitin-protein ligase UHRF2
B: E3 ubiquitin-protein ligase UHRF2
C: 5mC-containing DNA1
D: 5mC-containing DNA2


Theoretical massNumber of molelcules
Total (without water)58,4604
Polymers58,4604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-19 kcal/mol
Surface area20980 Å2
MethodPISA
2
E: E3 ubiquitin-protein ligase UHRF2
F: E3 ubiquitin-protein ligase UHRF2
G: 5mC-containing DNA1
H: 5mC-containing DNA2


Theoretical massNumber of molelcules
Total (without water)58,4604
Polymers58,4604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-21 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.331, 83.694, 83.686
Angle α, β, γ (deg.)89.97, 89.94, 90.02
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
E3 ubiquitin-protein ligase UHRF2 / Np95/ICBP90-like RING finger protein / Np95-like RING finger protein / Nuclear protein 97 / Nuclear ...Np95/ICBP90-like RING finger protein / Np95-like RING finger protein / Nuclear protein 97 / Nuclear zinc finger protein Np97 / RING finger protein 107 / Ubiquitin-like PHD and RING finger domain-containing protein 2 / Ubiquitin-like-containing PHD and RING finger domains protein 2


Mass: 25579.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF2, NIRF, RNF107 / Plasmid: pET28a-smt / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL
References: UniProt: Q96PU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: DNA chain 5mC-containing DNA1


Mass: 3708.429 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5mC-containing DNA2


Mass: 3592.358 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 932 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% ethanol and 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 11, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 77335 / Num. obs: 75805 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2 / Num. unique all: 7677 / % possible all: 97

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1491)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OLN

3oln


Resolution: 2.001→28.05 Å / SU ML: 0.22 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 20.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 3802 5.02 %RANDOM
Rwork0.1634 ---
all0.166 77335 --
obs0.1657 75755 97.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 2.001→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6107 974 0 932 8013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067554
X-RAY DIFFRACTIONf_angle_d0.96310480
X-RAY DIFFRACTIONf_dihedral_angle_d17.6532925
X-RAY DIFFRACTIONf_chiral_restr0.0421087
X-RAY DIFFRACTIONf_plane_restr0.0041214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0012-2.02650.29881280.24642512X-RAY DIFFRACTION94
2.0265-2.05320.27611370.23112663X-RAY DIFFRACTION97
2.0532-2.08130.26641330.21732643X-RAY DIFFRACTION97
2.0813-2.1110.27551500.21242657X-RAY DIFFRACTION97
2.111-2.14250.29621340.21482641X-RAY DIFFRACTION97
2.1425-2.1760.22031510.18932644X-RAY DIFFRACTION97
2.176-2.21160.26461440.19222641X-RAY DIFFRACTION97
2.2116-2.24980.22591420.19412627X-RAY DIFFRACTION97
2.2498-2.29060.25421440.18922658X-RAY DIFFRACTION97
2.2906-2.33470.25041460.18652734X-RAY DIFFRACTION98
2.3347-2.38230.20941450.18732575X-RAY DIFFRACTION98
2.3823-2.43410.23731240.18272622X-RAY DIFFRACTION98
2.4341-2.49070.24911180.18052720X-RAY DIFFRACTION98
2.4907-2.55290.24411420.16722663X-RAY DIFFRACTION98
2.5529-2.62190.21221680.16512696X-RAY DIFFRACTION98
2.6219-2.6990.21281490.16642671X-RAY DIFFRACTION98
2.699-2.7860.20081460.15872636X-RAY DIFFRACTION98
2.786-2.88550.21351380.1662665X-RAY DIFFRACTION98
2.8855-3.00090.20621490.15732697X-RAY DIFFRACTION99
3.0009-3.13730.2131360.16182700X-RAY DIFFRACTION99
3.1373-3.30250.19381350.14352699X-RAY DIFFRACTION99
3.3025-3.5090.15861300.14242690X-RAY DIFFRACTION99
3.509-3.77940.18171280.12842701X-RAY DIFFRACTION99
3.7794-4.15860.17951480.12982686X-RAY DIFFRACTION99
4.1586-4.75780.16811540.11912720X-RAY DIFFRACTION99
4.7578-5.98480.18941490.15492729X-RAY DIFFRACTION100
5.9848-28.05240.1971340.16472663X-RAY DIFFRACTION98

+
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