[English] 日本語
Yorodumi
- PDB-1yrv: Novel Ubiquitin-Conjugating Enzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yrv
TitleNovel Ubiquitin-Conjugating Enzyme
Componentsubiquitin-conjugating ligase MGC351130
KeywordsLIGASE / STRUCTURAL GENOMICS CONSORTIUM / SGC / UBIQUITIN / UBIQUITIN-CONJUGATING ENZYME
Function / homology
Function and homology information


HULC complex / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA repair / ATP binding
Similarity search - Function
: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 ...: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 U
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsWalker, J.R. / Choe, J. / Avvakumov, G.V. / Newman, E.M. / MacKenzie, F. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Mol Cell Proteomics / Year: 2012
Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.
Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S.
History
DepositionFeb 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 28, 2012Group: Database references
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ubiquitin-conjugating ligase MGC351130


Theoretical massNumber of molelcules
Total (without water)19,4521
Polymers19,4521
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.968, 74.009, 119.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-151-

HOH

21A-152-

HOH

31A-195-

HOH

-
Components

#1: Protein ubiquitin-conjugating ligase MGC351130 / E.C.6.3.2.19


Mass: 19452.154 Da / Num. of mol.: 1 / Fragment: residues 1-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: The N-terminal cloning tag MGSSHHHHHHSSGLVPRGS has not been removed from the protein
Gene: MGC35130 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5VVX9, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.96 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 298 K / pH: 7
Details: 10% PEG MME 5000, 5% Tacsimate, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.181→37.01 Å / Num. obs: 11277 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 5.78 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 20.3
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 5.22 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 4.1 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
AMoREphasing
REFMAC5.2refinement
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E2C

2e2c


Resolution: 2.18→35.13 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.904 / Rfactor Rfree error: 0.013 / SU B: 9.033 / SU ML: 0.223 / Data cutoff high absF: 1280277.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 539 4.8 %RANDOM
Rwork0.244 ---
obs0.2441 11276 98.1 %-
all-11277 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.7583 Å2 / ksol: 0.365431 e/Å3
Displacement parametersBiso mean: 55.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2--16.68 Å20 Å2
3----14.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.18→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 0 76 1320
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.842
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 2.18→2.32 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 88 5.2 %
Rwork0.38 1592 -
obs--89.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

+
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