+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-6693 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The resting state of yeast proteasome | |||||||||||||||||||||
![]() | ||||||||||||||||||||||
![]() |
| |||||||||||||||||||||
Function / homology | ![]() SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome ...SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / protein-containing complex localization / proteasome-activating activity / mitochondrial fission / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / nonfunctional rRNA decay / K48-linked polyubiquitin modification-dependent protein binding / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / peptide catabolic process / proteasome binding / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / regulation of protein catabolic process / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / 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 / Ub-specific processing proteases / threonine-type endopeptidase activity / mRNA export from nucleus / enzyme regulator activity / ERAD pathway / protein folding chaperone / Neutrophil degranulation / proteasome complex / ubiquitin binding / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / metallopeptidase activity / peroxisome / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / regulation of cell cycle / chromatin remodeling / protein domain specific binding / mRNA binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.3 Å | |||||||||||||||||||||
![]() | Ding Z / Cong Y | |||||||||||||||||||||
Funding support | ![]()
| |||||||||||||||||||||
![]() | ![]() Title: High-resolution cryo-EM structure of the proteasome in complex with ADP-AlFx. Authors: Zhanyu Ding / Zhenglin Fu / Cong Xu / Yifan Wang / Yanxing Wang / Junrui Li / Liangliang Kong / Jinhuan Chen / Na Li / Rongguang Zhang / Yao Cong / ![]() Abstract: The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic- ...The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic-resolution cryo-EM map of the S. cerevisiae 26S proteasome in complex with ADP-AlFx. Our biochemical and structural data reveal that the proteasome-ADP-AlFx is in an activated state, displaying a distinct conformational configuration especially in the AAA-ATPase motor region. Noteworthy, this map demonstrates an asymmetric nucleotide binding pattern with four consecutive AAA-ATPase subunits bound with nucleotide. The remaining two subunits, Rpt2 and Rpt6, with empty or only partially occupied nucleotide pocket exhibit pronounced conformational changes in the AAA-ATPase ring, which may represent a collective result of allosteric cooperativity of all the AAA-ATPase subunits responding to ATP hydrolysis. This collective motion of Rpt2 and Rpt6 results in an elevation of their pore loops, which could play an important role in substrate processing of proteasome. Our data also imply that the nucleotide occupancy pattern could be related to the activation status of the complex. Moreover, the HbYX tail insertion may not be sufficient to maintain the gate opening of 20S core particle. Our results provide new insights into the mechanisms of nucleotide-driven allosteric cooperativity of the complex and of the substrate processing by the proteasome. | |||||||||||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 10.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 48.2 KB 48.2 KB | Display Display | ![]() |
Images | ![]() | 51.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wviMC ![]() 6694C ![]() 5wvkC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.318 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : The yeast resting state proteasome
+Supramolecule #1: The yeast resting state proteasome
+Macromolecule #1: 26S protease regulatory subunit 4 homolog
+Macromolecule #2: 26S protease regulatory subunit 6B homolog
+Macromolecule #3: Proteasome subunit beta type-2
+Macromolecule #4: Proteasome subunit alpha type-1
+Macromolecule #5: Proteasome subunit beta type-3
+Macromolecule #6: Probable proteasome subunit alpha type-7
+Macromolecule #7: Proteasome subunit alpha type-6
+Macromolecule #8: Proteasome subunit alpha type-5
+Macromolecule #9: Proteasome subunit alpha type-4
+Macromolecule #10: 26S proteasome complex subunit SEM1
+Macromolecule #11: 26S proteasome regulatory subunit RPN2
+Macromolecule #12: 26S proteasome regulatory subunit RPN3
+Macromolecule #13: 26S proteasome regulatory subunit RPN12
+Macromolecule #14: 26S proteasome regulatory subunit RPN7
+Macromolecule #15: 26S proteasome regulatory subunit RPN6
+Macromolecule #16: 26S protease regulatory subunit 8 homolog
+Macromolecule #17: 26S protease subunit RPT4
+Macromolecule #18: 26S protease regulatory subunit 6A
+Macromolecule #19: 26S proteasome regulatory subunit RPN8
+Macromolecule #20: 26S proteasome regulatory subunit RPN10
+Macromolecule #21: 26S proteasome regulatory subunit RPN9
+Macromolecule #22: 26S proteasome regulatory subunit RPN5
+Macromolecule #23: 26S protease regulatory subunit 7 homolog
+Macromolecule #24: Proteasome subunit alpha type-3
+Macromolecule #25: Proteasome subunit alpha type-2
+Macromolecule #26: Proteasome subunit beta type-1
+Macromolecule #27: Proteasome subunit beta type-4
+Macromolecule #28: Proteasome subunit beta type-5
+Macromolecule #29: Proteasome subunit beta type-6
+Macromolecule #30: Proteasome subunit beta type-7
+Macromolecule #31: 26S proteasome regulatory subunit RPN13
+Macromolecule #32: 26S proteasome regulatory subunit RPN1
+Macromolecule #33: Ubiquitin carboxyl-terminal hydrolase RPN11
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | cell |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26000 |
---|---|
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |