[English] 日本語
Yorodumi
- PDB-7yw1: crystal structure of UBE2O -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yw1
Titlecrystal structure of UBE2O
Components(E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
KeywordsCYTOSOLIC PROTEIN / UBE2O
Function / homologyUbiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
Function and homology information
Biological speciesTrametes pubescens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsFu, Z. / Zhu, W. / Huang, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: crystal structure of UBE2O
Authors: Fu, Z. / Zhu, W. / Huang, H.
History
DepositionAug 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
B: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O


Theoretical massNumber of molelcules
Total (without water)205,8862
Polymers205,8862
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.320, 132.529, 155.036
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

#1: Protein (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O


Mass: 102942.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes pubescens (fungus) / Gene: TRAPUB_10883 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1M2VY70

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / Details: PEG MME 5000, Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97913697371156 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913697371156 Å / Relative weight: 1
ReflectionResolution: 3.27→100.74 Å / Num. obs: 28617 / % possible obs: 92 % / Redundancy: 12.8 % / CC1/2: 0.996 / Net I/σ(I): 9.5
Reflection shellResolution: 3.27→3.56 Å / Num. unique obs: 1431 / CC1/2: 0.604

-
Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
PHENIXphasing
STARANISOdata scaling
PDB_EXTRACTdata extraction
PROCORdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 prediction

Resolution: 3.27→54.04 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.3002 --
Rwork0.2495 --
obs-28589 76.62 %
Refinement stepCycle: LAST / Resolution: 3.27→54.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10032 0 0 0 10032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001610229
X-RAY DIFFRACTIONf_angle_d0.442413981
X-RAY DIFFRACTIONf_chiral_restr0.04031642
X-RAY DIFFRACTIONf_plane_restr0.00371810
X-RAY DIFFRACTIONf_dihedral_angle_d3.5121447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.27-3.390.492590.3492323X-RAY DIFFRACTION9.01
3.39-3.530.35440.3172740X-RAY DIFFRACTION21.34
3.53-3.690.3623740.30961533X-RAY DIFFRACTION43.92
3.69-3.880.3641400.29283152X-RAY DIFFRACTION89.31
3.88-4.120.34551530.26553541X-RAY DIFFRACTION99.92
4.12-4.440.26431530.23193559X-RAY DIFFRACTION100
4.44-4.890.28311950.22153530X-RAY DIFFRACTION99.97
4.89-5.590.28251700.24213563X-RAY DIFFRACTION100
5.6-7.050.33712080.27553582X-RAY DIFFRACTION99.97
7.05-54.040.26862030.23083717X-RAY DIFFRACTION99.47

+
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