[English] 日本語
Yorodumi
- PDB-8fxf: Crystal structure of the coiled-coil domain of TRIM56 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fxf
TitleCrystal structure of the coiled-coil domain of TRIM56
ComponentsE3 ubiquitin-protein ligase TRIM56
KeywordsLIGASE / Ubiquitination / coiled-coil
Function / homology
Function and homology information


Regulation of innate immune responses to cytosolic DNA / suppression of viral release by host / negative regulation of viral entry into host cell / response to type I interferon / positive regulation of type I interferon-mediated signaling pathway / protein monoubiquitination / protein K63-linked ubiquitination / positive regulation of interferon-beta production / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity ...Regulation of innate immune responses to cytosolic DNA / suppression of viral release by host / negative regulation of viral entry into host cell / response to type I interferon / positive regulation of type I interferon-mediated signaling pathway / protein monoubiquitination / protein K63-linked ubiquitination / positive regulation of interferon-beta production / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / defense response to virus / innate immune response / zinc ion binding / cytoplasm
Similarity search - Function
: / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-box 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 finger, RING-type, conserved site / Zinc finger RING-type signature. ...: / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-box 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 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
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM56
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLou, X.H. / Ma, B.B. / Zhuang, Y. / Li, X.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI080779 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI155488 United States
CitationJournal: Comput Struct Biotechnol J / Year: 2023
Title: TRIM56 coiled-coil domain structure provides insights into its E3 ligase functions.
Authors: Lou, X. / Ma, B. / Zhuang, Y. / Xiao, X. / Minze, L.J. / Xing, J. / Zhang, Z. / Li, X.C.
History
DepositionJan 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM56
B: E3 ubiquitin-protein ligase TRIM56
C: E3 ubiquitin-protein ligase TRIM56
D: E3 ubiquitin-protein ligase TRIM56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3605
Polymers40,1214
Non-polymers2381
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS was used to confirm the tetramer existed in the crystallographic packing.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-94 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.679, 136.679, 65.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein
E3 ubiquitin-protein ligase TRIM56 / Tripartite motif-containing protein 56


Mass: 10030.315 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trim56 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q80VI1, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.62 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 10% Glycerol, 5% PEG3000, 30%PEG400, 0.1M Hepes pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→48 Å / Num. obs: 14908 / % possible obs: 99.4 % / Redundancy: 3.7 % / CC1/2: 0.999 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 2153 / CC1/2: 0.678

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UG2

7ug2


Resolution: 2.8→44.655 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: FREE R-VALUE / ESU R: 0.477 / ESU R Free: 0.316 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2644 753 5.052 %
Rwork0.2194 14151 -
all0.222 --
obs-14904 99.228 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 102.779 Å2
Baniso -1Baniso -2Baniso -3
1-1.489 Å20 Å20 Å2
2--1.489 Å20 Å2
3----2.979 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 15 0 2425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122473
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.6423333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5625320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.619528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.45710502
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.60410125
X-RAY DIFFRACTIONr_chiral_restr0.1390.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021772
X-RAY DIFFRACTIONr_nbd_refined0.2540.21131
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21653
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.246
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3070.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2870.23
X-RAY DIFFRACTIONr_mcbond_it11.2869.9511268
X-RAY DIFFRACTIONr_mcangle_it16.13514.921586
X-RAY DIFFRACTIONr_scbond_it13.47310.4931205
X-RAY DIFFRACTIONr_scangle_it18.69415.3871745
X-RAY DIFFRACTIONr_lrange_it22.356208.04210098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.8-2.8720.395730.37810120.37911060.8950.90898.10130.378
2.872-2.9510.389440.34910180.3510620.8850.9181000.332
2.951-3.0360.359460.3189890.31910380.9330.93399.7110.308
3.036-3.1290.467460.3049590.31110090.8810.94399.60360.284
3.129-3.2310.378400.2889340.2919800.9160.95399.38780.273
3.231-3.3440.252460.2768990.2759520.9720.95699.26470.258
3.344-3.4690.303560.2468590.259190.9490.96799.56470.23
3.469-3.610.32530.2458320.2498950.9350.96698.88270.231
3.61-3.7690.309460.2257870.2298470.9490.9798.34710.218
3.769-3.9520.202390.2047680.2048100.9720.97599.62960.2
3.952-4.1640.232360.1947260.1967630.9650.97899.86890.197
4.164-4.4140.233330.2047100.2057470.9660.97799.46450.218
4.414-4.7160.225230.1856500.1866780.9750.98199.26250.2
4.716-5.0890.209440.2076050.2076590.9720.97698.48260.222
5.089-5.5670.367290.2665450.2715800.9290.95798.96550.276
5.567-6.2120.406340.2845090.295430.9040.9541000.287
6.212-7.150.22210.2384620.2374850.9750.9799.58760.272
7.15-8.7020.195160.153930.1514120.980.98899.27180.193
8.702-12.0790.221210.1352990.143280.9750.99197.5610.188
12.079-44.6550.16670.2271950.2252030.9860.97199.50740.272

+
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