[English] 日本語
Yorodumi
- EMDB-31152: Reconstituted proteoliposomes of TRIM72 in positive curvature #2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31152
TitleReconstituted proteoliposomes of TRIM72 in positive curvature #2
Map dataReconstituted proteoliposomes of TRIM72 in positive curvature #2
Sample
  • Complex: TRIM72 complex with phosphatidylserine-enriched liposomes.
    • Protein or peptide: TRIM72
KeywordsTRIM / Tripartite motif / Ubiquitin ligase / Coiled coil / B-box / PRY-SPRY / Membrane protein / LIGASE / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsPark SH / Song HK
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structure and activation of the RING E3 ubiquitin ligase TRIM72 on the membrane.
Authors: Si Hoon Park / Juhyun Han / Byung-Cheon Jeong / Ju Han Song / Se Hwan Jang / Hyeongseop Jeong / Bong Heon Kim / Young-Gyu Ko / Zee-Yong Park / Kyung Eun Lee / Jaekyung Hyun / Hyun Kyu Song /
Abstract: Defects in plasma membrane repair can lead to muscle and heart diseases in humans. Tripartite motif-containing protein (TRIM)72 (mitsugumin 53; MG53) has been determined to rapidly nucleate vesicles ...Defects in plasma membrane repair can lead to muscle and heart diseases in humans. Tripartite motif-containing protein (TRIM)72 (mitsugumin 53; MG53) has been determined to rapidly nucleate vesicles at the site of membrane damage, but the underlying molecular mechanisms remain poorly understood. Here we present the structure of Mus musculus TRIM72, a complete model of a TRIM E3 ubiquitin ligase. We demonstrated that the interaction between TRIM72 and phosphatidylserine-enriched membranes is necessary for its oligomeric assembly and ubiquitination activity. Using cryogenic electron tomography and subtomogram averaging, we elucidated a higher-order model of TRIM72 assembly on the phospholipid bilayer. Combining structural and biochemical techniques, we developed a working molecular model of TRIM72, providing insights into the regulation of RING-type E3 ligases through the cooperation of multiple domains in higher-order assemblies. Our findings establish a fundamental basis for the study of TRIM E3 ligases and have therapeutic implications for diseases associated with membrane repair.
History
DepositionApr 1, 2021-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_31152.png

Downloads & links

-
Map

FileDownload / File: emd_31152.map.gz / Format: CCP4 / Size: 1.7 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationReconstituted proteoliposomes of TRIM72 in positive curvature #2
Voxel sizeX=Y=Z: 5.6 Å
Density
Minimum - Maximum-128.0 - 120.0
Average (Standard dev.)-2.4997702 (±23.968817000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin176227-44
Dimensions16822945
Spacing22916845
CellA: 1282.4 Å / B: 940.8 Å / C: 252.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : TRIM72 complex with phosphatidylserine-enriched liposomes.

EntireName: TRIM72 complex with phosphatidylserine-enriched liposomes.
Components
  • Complex: TRIM72 complex with phosphatidylserine-enriched liposomes.
    • Protein or peptide: TRIM72

-
Supramolecule #1: TRIM72 complex with phosphatidylserine-enriched liposomes.

SupramoleculeName: TRIM72 complex with phosphatidylserine-enriched liposomes.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: TRIM72

MacromoleculeName: TRIM72 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSAAPGLLRQ ELSCPLCLQL FDAPVTAECG HSFCRACLIR VAGEPAADGT VACPCCQAPT RPQALSTNL QLSRLVEGLA QVPQGHCEEH LDPLSIYCEQ DRTLVCGVCA SLGSHRGHRL L PAAEAQAR LKTQLPQQKM QLQEACMRKE KTVAVLEHQL VEVEETVRQF ...String:
GSAAPGLLRQ ELSCPLCLQL FDAPVTAECG HSFCRACLIR VAGEPAADGT VACPCCQAPT RPQALSTNL QLSRLVEGLA QVPQGHCEEH LDPLSIYCEQ DRTLVCGVCA SLGSHRGHRL L PAAEAQAR LKTQLPQQKM QLQEACMRKE KTVAVLEHQL VEVEETVRQF RGAVGEQLGK MR MFLAALE SSLDREAERV RGDAGVALRR ELSSLNSYLE QLRQMEKVLE EVADKPQTEF LMK FCLVTS RLQKILSESP PPARLDIQLP VISDDFKFQV WKKMFRALMP ALEELTFDPS SAHP SLVVS SSGRRVECSD QKAPPAGEDT RQFDKAVAVV AQQLLSQGEH YWEVEVGDKP RWALG VMAA DASRRGRLHA VPSQGLWLLG LRDGKILEAH VEAKEPRALR TPERPPARIG LYLSFA DGV LAFYDASNPD VLTPIFSFHE RLPGPVYPIF DVCWHDKGKN AQPLLLVGPE QEQA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionNumber images used: 61

+
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