[English] 日本語
Yorodumi
- PDB-5fey: TRIM32 RING -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fey
TitleTRIM32 RING
ComponentsE3 ubiquitin-protein ligase TRIM32
KeywordsLIGASE / E3 ligase / ubiquitin
Function / homology
Function and homology information


actin ubiquitination / positive regulation of interleukin-17-mediated signaling pathway / positive regulation of chemokine (C-C motif) ligand 20 production / striated muscle myosin thick filament / positive regulation of striated muscle cell differentiation / suppression of viral release by host / free ubiquitin chain polymerization / negative regulation of toll-like receptor 4 signaling pathway / negative regulation of cilium assembly / Tat protein binding ...actin ubiquitination / positive regulation of interleukin-17-mediated signaling pathway / positive regulation of chemokine (C-C motif) ligand 20 production / striated muscle myosin thick filament / positive regulation of striated muscle cell differentiation / suppression of viral release by host / free ubiquitin chain polymerization / negative regulation of toll-like receptor 4 signaling pathway / negative regulation of cilium assembly / Tat protein binding / positive regulation of autophagosome assembly / tissue homeostasis / negative regulation of viral transcription / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of cell motility / positive regulation of neurogenesis / muscle cell cellular homeostasis / myosin binding / axon development / fat cell differentiation / response to starvation / protein K63-linked ubiquitination / positive regulation of proteolysis / autophagosome / response to tumor necrosis factor / protein K48-linked ubiquitination / positive regulation of autophagy / positive regulation of cell cycle / response to UV / negative regulation of fibroblast proliferation / translation initiation factor binding / Regulation of innate immune responses to cytosolic DNA / positive regulation of neuron differentiation / ubiquitin binding / RING-type E3 ubiquitin transferase / positive regulation of DNA-binding transcription factor activity / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / : / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / ubiquitin-dependent protein catabolic process / positive regulation of cell growth / positive regulation of canonical NF-kappaB signal transduction / response to oxidative stress / transcription coactivator activity / protein ubiquitination / positive regulation of cell migration / innate immune response / centrosome / endoplasmic reticulum / mitochondrion / RNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / NHL repeat profile. / NHL repeat / NHL repeat / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like ...: / NHL repeat profile. / NHL repeat / NHL repeat / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM32
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.23 Å
AuthorsRittinger, K. / Esposito, D. / Koliopoulos, M.G.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U117565398 United Kingdom
The Francis Crick InstituteFCI01 United Kingdom
CitationJournal: Embo J. / Year: 2016
Title: Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity.
Authors: Koliopoulos, M.G. / Esposito, D. / Christodoulou, E. / Taylor, I.A. / Rittinger, K.
History
DepositionDec 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 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: E3 ubiquitin-protein ligase TRIM32
B: E3 ubiquitin-protein ligase TRIM32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6616
Polymers21,3992
Non-polymers2624
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-15 kcal/mol
Surface area9300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.536, 54.536, 99.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein E3 ubiquitin-protein ligase TRIM32 / 72 kDa Tat-interacting protein / Tripartite motif-containing protein 32 / Zinc finger protein HT2A ...72 kDa Tat-interacting protein / Tripartite motif-containing protein 32 / Zinc finger protein HT2A / TRIM32-RING


Mass: 10699.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM32, HT2A / Production host: Escherichia coli (E. coli)
References: UniProt: Q13049, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0 and 5 % PEG 600

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.28254 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28254 Å / Relative weight: 1
ReflectionResolution: 2.23→47.781 Å / Num. obs: 7770 / % possible obs: 99.63 % / Redundancy: 20 % / Rmerge(I) obs: 0.1401 / Net I/σ(I): 13.28
Reflection shellRmerge(I) obs: 0.962

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementResolution: 2.23→47.781 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 402 5.18 %
Rwork0.2479 --
obs0.249 7764 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.23→47.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 4 27 1254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021234
X-RAY DIFFRACTIONf_angle_d0.4861661
X-RAY DIFFRACTIONf_dihedral_angle_d15.109775
X-RAY DIFFRACTIONf_chiral_restr0.037210
X-RAY DIFFRACTIONf_plane_restr0.003206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2302-2.55290.40571320.32992362X-RAY DIFFRACTION99
2.5529-3.21620.32271320.30892434X-RAY DIFFRACTION100
3.2162-47.79220.23871380.22042566X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.8889-1.2754-1.57248.04961.77536.46870.15260.9211-0.529-0.3360.222-1.07280.36970.88-0.20730.3950.0793-0.0310.7945-0.20980.519224.970812.882833.0567
28.27090.23341.86877.01610.48912.2145-0.20670.60710.3035-0.77550.25421.07660.0142-0.6306-0.05070.4954-0.0313-0.06990.53470.07470.48097.817816.474831.0638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 85)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 82)

+
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://pdbjlvh1.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