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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3916 | |||||||||||||||
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Title | Ground state 26S proteasome (GS1) | |||||||||||||||
![]() | in situ reconstruction of Rat proteasome in Ground State 1 | |||||||||||||||
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![]() | UPS / Ground state / Neuron degeneration / HYDROLASE | |||||||||||||||
Function / homology | ![]() nuclear proteasome complex / Cross-presentation of soluble exogenous antigens (endosomes) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of ornithine decarboxylase (ODC) / Metalloprotease DUBs / Assembly of the pre-replicative complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C ...nuclear proteasome complex / Cross-presentation of soluble exogenous antigens (endosomes) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of ornithine decarboxylase (ODC) / Metalloprotease DUBs / Assembly of the pre-replicative complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / UCH proteinases / CDK-mediated phosphorylation and removal of Cdc6 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / The role of GTSE1 in G2/M progression after G2 checkpoint / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX3 expression and activity / GLI3 is processed to GLI3R by the proteasome / Activation of NF-kappaB in B cells / Degradation of beta-catenin by the destruction complex / Degradation of AXIN / Regulation of RAS by GAPs / Orc1 removal from chromatin / Neddylation / AUF1 (hnRNP D0) binds and destabilizes mRNA / MAPK6/MAPK4 signaling / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / Separation of Sister Chromatids / fluid transport / Antigen processing: Ubiquitination & Proteasome degradation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / ABC-family proteins mediated transport / Ub-specific processing proteases / positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / proteasome accessory complex / integrator complex / meiosis I / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / proteasome core complex / Neutrophil degranulation / immune system process / myofibril / proteasome binding / regulation of protein catabolic process / proteasome storage granule / blastocyst development / general transcription initiation factor binding / NF-kappaB binding / endopeptidase activator activity / polyubiquitin modification-dependent protein binding / proteasome assembly / proteasome endopeptidase complex / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / mRNA export from nucleus / enzyme regulator activity / regulation of proteasomal protein catabolic process / ERAD pathway / inclusion body / negative regulation of inflammatory response to antigenic stimulus / : / TBP-class protein binding / sarcomere / proteasome complex / ciliary basal body / proteolysis involved in protein catabolic process / stem cell differentiation / lipopolysaccharide binding / P-body / double-strand break repair via homologous recombination / response to virus / modulation of chemical synaptic transmission / response to organic cyclic compound / nuclear matrix / double-strand break repair via nonhomologous end joining Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 11.8 Å | |||||||||||||||
![]() | Guo Q / Lehmer C | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment. Authors: Qiang Guo / Carina Lehmer / Antonio Martínez-Sánchez / Till Rudack / Florian Beck / Hannelore Hartmann / Manuela Pérez-Berlanga / Frédéric Frottin / Mark S Hipp / F Ulrich Hartl / ...Authors: Qiang Guo / Carina Lehmer / Antonio Martínez-Sánchez / Till Rudack / Florian Beck / Hannelore Hartmann / Manuela Pérez-Berlanga / Frédéric Frottin / Mark S Hipp / F Ulrich Hartl / Dieter Edbauer / Wolfgang Baumeister / Rubén Fernández-Busnadiego / ![]() ![]() Abstract: Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo- ...Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo-electron tomography to dissect the molecular architecture of protein aggregates within intact neurons at high resolution. We focus on the poly-Gly-Ala (poly-GA) aggregates resulting from aberrant translation of an expanded GGGGCC repeat in C9orf72, the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. We find that poly-GA aggregates consist of densely packed twisted ribbons that recruit numerous 26S proteasome complexes, while other macromolecules are largely excluded. Proximity to poly-GA ribbons stabilizes a transient substrate-processing conformation of the 26S proteasome, suggesting stalled degradation. Thus, poly-GA aggregates may compromise neuronal proteostasis by driving the accumulation and functional impairment of a large fraction of cellular proteasomes. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 52 KB 52 KB | Display Display | ![]() |
Images | ![]() | 58.9 KB | ||
Filedesc metadata | ![]() | 14.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6epfMC ![]() 3913C ![]() 3914C ![]() 3915C ![]() 3917C ![]() 4191C ![]() 6epcC ![]() 6epdC ![]() 6epeC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | in situ reconstruction of Rat proteasome in Ground State 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Ground state 26S proteasome (GS1)
+Supramolecule #1: Ground state 26S proteasome (GS1)
+Macromolecule #1: Proteasome subunit alpha type-6
+Macromolecule #2: Proteasome subunit alpha type-2
+Macromolecule #3: Proteasome subunit alpha type-4
+Macromolecule #4: Proteasome subunit alpha type-7
+Macromolecule #5: Proteasome subunit alpha type-5
+Macromolecule #6: Proteasome subunit alpha type-1
+Macromolecule #7: Proteasome subunit alpha type-3
+Macromolecule #8: Proteasome subunit beta type-6
+Macromolecule #9: Proteasome subunit beta type-7
+Macromolecule #10: Proteasome subunit beta type-3
+Macromolecule #11: Proteasome subunit beta type-2
+Macromolecule #12: Proteasome subunit beta type-5
+Macromolecule #13: Proteasome subunit beta type-1
+Macromolecule #14: Proteasome subunit beta type-4
+Macromolecule #15: 26S proteasome subunit S5a
+Macromolecule #16: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 14
+Macromolecule #17: Proteasome 26S subunit, non-ATPase 8
+Macromolecule #18: RCG28037
+Macromolecule #19: 26S proteasome non-ATPase regulatory subunit 2
+Macromolecule #20: 26S proteasome non-ATPase regulatory subunit 1
+Macromolecule #21: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 3
+Macromolecule #22: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 12
+Macromolecule #23: 26S proteasome non-ATPase regulatory subunit 11
+Macromolecule #24: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 6
+Macromolecule #25: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 7 (Predicted)
+Macromolecule #26: 26S proteasome non-ATPase regulatory subunit 13
+Macromolecule #27: 26S proteasome regulatory subunit 7
+Macromolecule #28: 26S proteasome regulatory subunit 4
+Macromolecule #29: 26S proteasome regulatory subunit 6B
+Macromolecule #30: Proteasome 26S subunit, ATPase 6
+Macromolecule #31: 26S proteasome regulatory subunit 6A
+Macromolecule #32: 26S proteasome regulatory subunit 8
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: The grid was coated with C prior to use |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
Details | FIB milled rat primary neurons |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average exposure time: 2.4 sec. / Average electron dose: 1.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 11.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number subtomograms used: 7393 |
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Extraction | Number tomograms: 9 / Number images used: 10367 / Reference model: average of manual picked subtomograms / Method: Template matching / Software: (Name: PyTom, TOM Toolbox, RELION (ver. 1.4)) |
Final 3D classification | Number classes: 4 / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-6epf: |