[English] 日本語
Yorodumi
- PDB-2lvn: Structure of the gp78 CUE domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lvn
TitleStructure of the gp78 CUE domain
ComponentsE3 ubiquitin-protein ligase AMFR
KeywordsLIGASE / CUE domain
Function / homology
Function and homology information


regulation of SREBP signaling pathway / positive regulation of plant-type hypersensitive response / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / Derlin-1 retrotranslocation complex / BAT3 complex binding / ubiquitin-ubiquitin ligase activity / ubiquitin-specific protease binding / ERAD pathway / non-canonical NF-kappaB signal transduction ...regulation of SREBP signaling pathway / positive regulation of plant-type hypersensitive response / RING-type E3 ubiquitin transferase (cysteine targeting) / protein K27-linked ubiquitination / Derlin-1 retrotranslocation complex / BAT3 complex binding / ubiquitin-ubiquitin ligase activity / ubiquitin-specific protease binding / ERAD pathway / non-canonical NF-kappaB signal transduction / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / ER Quality Control Compartment (ERQC) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein-macromolecule adaptor activity / signaling receptor activity / protein-folding chaperone binding / growth cone / ubiquitin-dependent protein catabolic process / learning or memory / neuronal cell body / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / signal transduction / protein-containing complex / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase AMFR, Ube2g2-binding region / E3 gp78 Ube2g2-binding region (G2BR) / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Ring finger domain / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Ring finger ...E3 ubiquitin-protein ligase AMFR, Ube2g2-binding region / E3 gp78 Ube2g2-binding region (G2BR) / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Ring finger domain / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase AMFR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLiu, S. / Chen, Y. / Huang, T. / Tarasov, S.G. / King, A. / Li, J. / Weissman, A.M. / Byrd, R.A. / Das, R.
CitationJournal: Structure / Year: 2012
Title: Promiscuous Interactions of gp78 E3 Ligase CUE Domain with Polyubiquitin Chains.
Authors: Liu, S. / Chen, Y. / Li, J. / Huang, T. / Tarasov, S. / King, A. / Weissman, A.M. / Byrd, R.A. / Das, R.
History
DepositionJul 9, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: E3 ubiquitin-protein ligase AMFR


Theoretical massNumber of molelcules
Total (without water)5,9671
Polymers5,9671
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein E3 ubiquitin-protein ligase AMFR / Autocrine motility factor receptor / isoform 2 / AMF receptor / isoform 2 / RING finger protein 45 / gp78


Mass: 5966.752 Da / Num. of mol.: 1 / Fragment: CUE domain residues 453-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMFR, RNF45 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UKV5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR / Details: 1H, 13C, 15N assignments of gp78 CUE domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D C(CO)NH
1613D H(CCO)NH
1713D HN(CA)CB
1812D 1H-13C HSQC aromatic
1913D 1H-15N NOESY

-
Sample preparation

DetailsContents: 50 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMTRIS-11
50 mMsodium chloride-21
Sample conditionspH: 7.2 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker INOVABrukerINOVA6001
Bruker INOVABrukerINOVA7002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA8004

-
Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: FINAL STEP IN WATER
NMR constraintsNOE constraints total: 1189 / NOE intraresidue total count: 282 / NOE long range total count: 102 / NOE medium range total count: 634 / NOE sequential total count: 171 / Protein phi angle constraints total count: 48 / Protein psi angle constraints total count: 49
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 1.8 Å / Maximum upper distance constraint violation: 6 Å
NMR ensemble rmsDistance rms dev: 0 Å

+
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