[English] 日本語
Yorodumi
- PDB-1fzy: CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE UBIQUITIN CONJUGATI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fzy
TitleCRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE UBIQUITIN CONJUGATING ENZYME 1
ComponentsUBIQUITIN-CONJUGATING ENZYME E2-24 KDA
KeywordsLIGASE / ALPHA-BETA ROLL
Function / homology
Function and homology information


Synthesis of active ubiquitin: roles of E1 and E2 enzymes / vesicle organization / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / ERAD pathway / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / vesicle organization / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / ERAD pathway / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / ATP binding / nucleus / cytosol
Similarity search - Function
Ubiquitin-conjugating enzyme, C-terminal fungi / Fungal ubiquitin-associated domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. ...Ubiquitin-conjugating enzyme, C-terminal fungi / Fungal ubiquitin-associated domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsGlover, M. / Williams, R.S.
CitationJournal: Structure / Year: 2001
Title: Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail.
Authors: Hamilton, K.S. / Ellison, M.J. / Barber, K.R. / Williams, R.S. / Huzil, J.T. / McKenna, S. / Ptak, C. / Glover, M. / Shaw, G.S.
History
DepositionOct 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 21, 2021Group: Data collection / Derived calculations / Refinement description
Category: refine / struct_biol / struct_sheet
Item: _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _struct_sheet.number_strands
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2-24 KDA
B: UBIQUITIN-CONJUGATING ENZYME E2-24 KDA


Theoretical massNumber of molelcules
Total (without water)33,3942
Polymers33,3942
Non-polymers00
Water5,098283
1
A: UBIQUITIN-CONJUGATING ENZYME E2-24 KDA


Theoretical massNumber of molelcules
Total (without water)16,6971
Polymers16,6971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UBIQUITIN-CONJUGATING ENZYME E2-24 KDA


Theoretical massNumber of molelcules
Total (without water)16,6971
Polymers16,6971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.166, 47.471, 75.776
Angle α, β, γ (deg.)90.00, 92.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer. A non-crystallographically related dimer is found in the asymmetric unit. The significance of this dimer interaction is unknown. The biological assembly is a monomer. A non-crystallographically related dimer is found in the asymmetric unit. The significance of this dimer interaction is unknown.

-
Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2-24 KDA


Mass: 16697.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P21734, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 5000-Monomethylether, Ammonium Sulphate, isopropanol, MES buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20-22 ℃ / pH: 7.5 / Method: vapor diffusion / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
220 mMHEPES1drop
3400 mM1dropNaCl
41 mMEDTA1drop
51 mMdithiothreitol1drop
627 %PEG5000 MME1reservoir
79 %isopropanol1reservoir
8100 mMammonium sulfate1reservoir
9100 mMMES1reservoir
105 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 23300 / Num. obs: 23300 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.345 / Num. unique all: 949 / % possible all: 81.1
Reflection
*PLUS
Num. measured all: 85242
Reflection shell
*PLUS
% possible obs: 81.1 % / Mean I/σ(I) obs: 3.5

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→20 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER (CNS)
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2301 -RANDOM
Rwork0.209 ---
obs0.209 23274 97.8 %-
all-23274 --
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2313 0 0 283 2596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0087
X-RAY DIFFRACTIONc_angle_deg1.274
X-RAY DIFFRACTIONc_improper_angle_d0.872
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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