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Yorodumi- EMDB-8663: Nucleotide-driven Triple-state Remodeling of the AAA-ATPase Chann... -
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-Basic information
Entry | Database: EMDB / ID: EMD-8663 | |||||||||
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Title | Nucleotide-driven Triple-state Remodeling of the AAA-ATPase Channel in the Activated Human 26S Proteasome | |||||||||
Map data | Final map of SD1 state corrected with a B-factor of -70 | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / purine ribonucleoside triphosphate binding / meiosis I / positive regulation of proteasomal protein catabolic process / proteasome regulatory particle / cytosolic proteasome complex ...positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / purine ribonucleoside triphosphate binding / meiosis I / positive regulation of proteasomal protein catabolic process / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / metal-dependent deubiquitinase activity / regulation of endopeptidase activity / negative regulation of programmed cell death / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / K63-linked deubiquitinase activity / immune system process / myofibril / proteasome binding / regulation of protein catabolic process / proteasome storage granule / transcription factor binding / 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 / enzyme regulator activity / regulation of proteasomal protein catabolic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / ERAD pathway / inclusion body / negative regulation of inflammatory response to antigenic stimulus / : / sarcomere / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / proteolysis involved in protein catabolic process / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / stem cell differentiation / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / lipopolysaccharide binding / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / P-body / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Orc1 removal from chromatin / double-strand break repair via homologous recombination / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / response to virus / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / response to organic cyclic compound / Metalloprotease DUBs / CLEC7A (Dectin-1) signaling / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Zhu Y / Wang WL / Yu D / Ouyang Q / Lu Y / Mao Y | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome. Authors: Yanan Zhu / Wei Li Wang / Daqi Yu / Qi Ouyang / Ying Lu / Youdong Mao / Abstract: The proteasome is a sophisticated ATP-dependent molecular machine responsible for protein degradation in all known eukaryotic cells. It remains elusive how conformational changes of the AAA-ATPase ...The proteasome is a sophisticated ATP-dependent molecular machine responsible for protein degradation in all known eukaryotic cells. It remains elusive how conformational changes of the AAA-ATPase unfoldase in the regulatory particle (RP) control the gating of the substrate-translocation channel leading to the proteolytic chamber of the core particle (CP). Here we report three alternative states of the ATP-γ-S-bound human proteasome, in which the CP gates are asymmetrically open, visualized by cryo-EM at near-atomic resolutions. At least four nucleotides are bound to the AAA-ATPase ring in these open-gate states. Variation in nucleotide binding gives rise to an axial movement of the pore loops narrowing the substrate-translation channel, which exhibit remarkable structural transitions between the spiral-staircase and saddle-shaped-circle topologies. Gate opening in the CP is thus regulated by nucleotide-driven conformational changes of the AAA-ATPase unfoldase. These findings demonstrate an elegant mechanism of allosteric coordination among sub-machines within the human proteasome holoenzyme. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8663.map.gz | 612.7 MB | EMDB map data format | |
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Header (meta data) | emd-8663-v30.xml emd-8663.xml | 56.2 KB 56.2 KB | Display Display | EMDB header |
Images | emd_8663.png | 62.7 KB | ||
Others | emd_8663_additional_1.map.gz emd_8663_additional_2.map.gz | 613.9 MB 592.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8663 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8663 | HTTPS FTP |
-Validation report
Summary document | emd_8663_validation.pdf.gz | 580.5 KB | Display | EMDB validaton report |
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Full document | emd_8663_full_validation.pdf.gz | 580.1 KB | Display | |
Data in XML | emd_8663_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_8663_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8663 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8663 | HTTPS FTP |
-Related structure data
Related structure data | 5vfpMC 8662C 8664C 8665C 8666C 8667C 8668C 5vfoC 5vfqC 5vfrC 5vfsC 5vftC 5vfuC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10090 (Title: Nucleotide-Driven Triple-State Remodeling of the AAA-ATPase Channel in the Activated Human 26S Proteasome Data size: 2.8 TB Data #1: Motion-corrected single frame micrographs of ATP-gS-bound human proteasome [micrographs - single frame] Data #2: Single-particle stacks of classified conformations [picked particles - multiframe - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8663.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Final map of SD1 state corrected with a B-factor of -70 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.75 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Final map of SD1 state with a local...
File | emd_8663_additional_1.map | ||||||||||||
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Annotation | Final map of SD1 state with a local mask of AAA-ATPase and 20S core particle | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Raw SD1 map
File | emd_8663_additional_2.map | ||||||||||||
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Annotation | Raw SD1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 26S proteasome bound to ATP-gammaS
+Supramolecule #1: 26S proteasome bound to ATP-gammaS
+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 non-ATPase regulatory subunit 1
+Macromolecule #16: 26S proteasome non-ATPase regulatory subunit 3
+Macromolecule #17: 26S proteasome non-ATPase regulatory subunit 12
+Macromolecule #18: 26S proteasome non-ATPase regulatory subunit 6
+Macromolecule #19: 26S proteasome non-ATPase regulatory subunit 7
+Macromolecule #20: 26S proteasome non-ATPase regulatory subunit 13
+Macromolecule #21: 26S proteasome non-ATPase regulatory subunit 4
+Macromolecule #22: 26S proteasome non-ATPase regulatory subunit 14
+Macromolecule #23: 26S proteasome non-ATPase regulatory subunit 8
+Macromolecule #24: sem1
+Macromolecule #25: 26S proteasome non-ATPase regulatory subunit 11
+Macromolecule #26: 26S proteasome regulatory subunit 7
+Macromolecule #27: 26S proteasome regulatory subunit 4
+Macromolecule #28: 26S proteasome regulatory subunit 8
+Macromolecule #29: 26S proteasome regulatory subunit 6B
+Macromolecule #30: 26S proteasome regulatory subunit 10B
+Macromolecule #31: 26S proteasome regulatory subunit 6A
+Macromolecule #32: 26S proteasome non-ATPase regulatory subunit 2
+Macromolecule #33: ZINC ION
+Macromolecule #34: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
-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 TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 10.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf (ver. 1.0) |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 66246 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.3) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3) |
-Atomic model buiding 1
Refinement | Space: REAL / Overall B value: 70 |
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Output model | PDB-5vfp: |