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- EMDB-33582: Higher-ordered assembly of mouse TRIM72 M138R on the Phosphatidyl... -

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Basic information

Entry
Database: EMDB / ID: EMD-33582
TitleHigher-ordered assembly of mouse TRIM72 M138R on the Phosphatidylserine/Cholesterol liposome bilayer
Map dataEM map
Sample
  • Complex: Higher-ordered assembly of mouse TRIM72 M138R on the Phosphatidylserine/Cholesterol liposome bilayer
    • Protein or peptide: Mouse TRIM72 M138R
KeywordsTRIM / Tripartite motif / Ubiquitin ligase / Coiled coil / B-box / PRY-SPRY / Membrane protein / LIGASE / METAL BINDING PROTEIN / Phosphatidylserine / TRIM72 / MG53
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 26.0 Å
AuthorsPark SH / Hyun J / Jeong H / Song HK
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
Other government Korea, Republic Of
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
DepositionJun 9, 2022-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33582.png

Downloads & links

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Map

FileDownload / File: emd_33582.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
2.3 Å/pix.
x 192 pix.
= 441.6 Å		2.3 Å/pix.
x 192 pix.
= 441.6 Å		2.3 Å/pix.
x 192 pix.
= 441.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.482
Minimum - Maximum-23.209430000000001 - 25.801327000000001
Average (Standard dev.)0.7747053 (±4.8921404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 441.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33582_msk_1.map
Projections & Slices
AxesZYX

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Half map: half map 1

Fileemd_33582_half_map_1.map
Annotationhalf map 1
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_33582_half_map_2.map
Annotationhalf map 2
Projections & Slices
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Sample components

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Entire : Higher-ordered assembly of mouse TRIM72 M138R on the Phosphatidyl...

EntireName: Higher-ordered assembly of mouse TRIM72 M138R on the Phosphatidylserine/Cholesterol liposome bilayer
Components
  • Complex: Higher-ordered assembly of mouse TRIM72 M138R on the Phosphatidylserine/Cholesterol liposome bilayer
    • Protein or peptide: Mouse TRIM72 M138R

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Supramolecule #1: Higher-ordered assembly of mouse TRIM72 M138R on the Phosphatidyl...

SupramoleculeName: Higher-ordered assembly of mouse TRIM72 M138R on the Phosphatidylserine/Cholesterol liposome bilayer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Higher-ordered assembly of mouse TRIM72 M138R on the Phosphatidylserine/Cholesterol liposome bilayer
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Mouse TRIM72 M138R

MacromoleculeName: Mouse TRIM72 M138R / 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 RPQALSTNLQ LSRLVEGLAQ VPQGHCEEH LDPLSIYCEQ DRTLVCGVCA SLGSHRGHRL LPAAEAQARL KTQLPQQKRQ LQEACMRKEK TVAVLEHQLV E VEETVRQF ...String:
GSAAPGLLRQ ELSCPLCLQL FDAPVTAECG HSFCRACLIR VAGEPAADGT VACPCCQAPT RPQALSTNLQ LSRLVEGLAQ VPQGHCEEH LDPLSIYCEQ DRTLVCGVCA SLGSHRGHRL LPAAEAQARL KTQLPQQKRQ LQEACMRKEK TVAVLEHQLV E VEETVRQF RGAVGEQLGK MRMFLAALES SLDREAERVR GDAGVALRRE LSSLNSYLEQ LRQMEKVLEE VADKPQTEFL MK FCLVTSR LQKILSESPP PARLDIQLPV ISDDFKFQVW KKMFRALMPA LEELTFDPSS AHPSLVVSSS GRRVECSDQK APP AGEDTR QFDKAVAVVA QQLLSQGEHY WEVEVGDKPR WALGVMAADA SRRGRLHAVP SQGLWLLGLR DGKILEAHVE AKEP RALRT PERPPARIGL YLSFADGVLA FYDASNPDVL TPIFSFHERL PGPVYPIFDV CWHDKGKNAQ PLLLVGPEQE QA

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state2D array

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Sample preparation

BufferpH: 8 / Details: 50 mM Tris-HCl pH 8.0 150 mM NaCl 1 mM TCEP
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 7 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.2 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 4033
ExtractionNumber tomograms: 1 / Number images used: 4033
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

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