+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33606 | ||||||||||||
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Title | Structure of human MG53 homo-dimer | ||||||||||||
Map data | Sharpened map | ||||||||||||
Sample |
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Function / homology | Function and homology information muscle system process / negative regulation of insulin-like growth factor receptor signaling pathway / negative regulation of myotube differentiation / plasma membrane repair / mitogen-activated protein kinase kinase kinase binding / ubiquitin conjugating enzyme binding / muscle organ development / phosphatidylserine binding / exocytosis / Smooth Muscle Contraction ...muscle system process / negative regulation of insulin-like growth factor receptor signaling pathway / negative regulation of myotube differentiation / plasma membrane repair / mitogen-activated protein kinase kinase kinase binding / ubiquitin conjugating enzyme binding / muscle organ development / phosphatidylserine binding / exocytosis / Smooth Muscle Contraction / negative regulation of insulin receptor signaling pathway / sarcolemma / cytoplasmic vesicle membrane / protein homooligomerization / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / zinc ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Chen L / Niu Y | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Biochem J / Year: 2022 Title: Cryo-EM structure of human MG53 homodimer. Authors: Yange Niu / Gengjia Chen / Fengxiang Lv / Rui-Ping Xiao / Xinli Hu / Lei Chen / Abstract: MG53 is a tripartite motif (TRIM) family E3 ligase and plays important biological functions. Here we present the cryo-EM structure of human MG53, showing that MG53 is a homodimer consisting of a ...MG53 is a tripartite motif (TRIM) family E3 ligase and plays important biological functions. Here we present the cryo-EM structure of human MG53, showing that MG53 is a homodimer consisting of a 'body' and two 'wings'. Intermolecular interactions are mainly distributed in the 'body' which is relatively stable, while two 'wings' are more dynamic. The overall architecture of MG53 is distinct from those of TRIM20 and TRIM25, illustrating the broad structural diversity of this protein family. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33606.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-33606-v30.xml emd-33606.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_33606.png | 60.6 KB | ||
Masks | emd_33606_msk_1.map | 64 MB | Mask map | |
Others | emd_33606_half_map_1.map.gz emd_33606_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33606 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33606 | HTTPS FTP |
-Related structure data
Related structure data | 7y4sMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33606.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33606_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_33606_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_33606_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human MG53 homo-dimer
Entire | Name: human MG53 homo-dimer |
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Components |
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-Supramolecule #1: human MG53 homo-dimer
Supramolecule | Name: human MG53 homo-dimer / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Tripartite motif-containing protein 72
Macromolecule | Name: Tripartite motif-containing protein 72 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 52.800512 KDa |
Recombinant expression | Organism: Escherichia coli B (bacteria) |
Sequence | String: MSAAPGLLHQ ELSCPLCLQL FDAPVTAECG HSFCRACLGR VAGEPAADGT VLCPCCQAPT RPQALSTNLQ LARLVEGLAQ VPQGHCEEH LDPLSIYCEQ DRALVCGVCA SLGSHRGHRL LPAAEAHARL KTQLPQQKLQ LQEACMRKEK SVAVLEHQLV E VEETVRQF ...String: MSAAPGLLHQ ELSCPLCLQL FDAPVTAECG HSFCRACLGR VAGEPAADGT VLCPCCQAPT RPQALSTNLQ LARLVEGLAQ VPQGHCEEH LDPLSIYCEQ DRALVCGVCA SLGSHRGHRL LPAAEAHARL KTQLPQQKLQ LQEACMRKEK SVAVLEHQLV E VEETVRQF RGAVGEQLGK MRVFLAALEG SLDREAERVR GEAGVALRRE LGSLNSYLEQ LRQMEKVLEE VADKPQTEFL MK YCLVTSR LQKILAESPP PARLDIQLPI ISDDFKFQVW RKMFRALMPA LEELTFDPSS AHPSLVVSSS GRRVECSEQK APP AGEDPR QFDKAVAVVA HQQLSEGEHY WEVDVGDKPR WALGVIAAEA PRRGRLHAVP SQGLWLLGLR EGKILEAHVE AKEP RALRS PERRPTRIGL YLSFGDGVLS FYDASDADAL VPLFAFHERL PRPVYPFFDV CWHDKGKNAQ PLLLVGPEGA EA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE / Details: ab initio |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.1.0) / Number images used: 125390 |