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- EMDB-31150: Reconstituted proteoliposomes of TRIM72 in negative curvature #2 -

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Basic information

Entry
Database: EMDB / ID: EMD-31150
TitleReconstituted proteoliposomes of TRIM72 in negative curvature #2
Map dataReconstituted proteoliposomes of TRIM72 in negative 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 5, 2022-
Map releaseOct 5, 2022-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31150.png

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Map

FileDownload / File: emd_31150.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationReconstituted proteoliposomes of TRIM72 in negative curvature #2
Voxel sizeX=Y=Z: 5.6 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)19.864522999999998 (±25.003579999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin716527-39
Dimensions24322644
Spacing22624344
CellA: 1265.6 Å / B: 1360.7999 Å / C: 246.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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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

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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)

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Macromolecule #1: TRIM72

MacromoleculeName: TRIM72 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
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

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

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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

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Image processing

Final reconstructionNumber images used: 61

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