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- EMDB-9217: Cryo-EM structures and dynamics of substrate-engaged human 26S pr... -
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Basic information
Entry | Database: EMDB / ID: EMD-9217 | ||||||||||||
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Title | Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome | ||||||||||||
![]() | The complete map of state EA2 of substrate-engaged human proteasome, low pass-filtered to 3 Angstrom without amplitude correction. | ||||||||||||
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![]() | Proteosome / HYDROLASE | ||||||||||||
Function / homology | ![]() thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / positive regulation of inclusion body assembly / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / integrator complex / purine ribonucleoside triphosphate binding ...thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / positive regulation of inclusion body assembly / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / integrator complex / purine ribonucleoside triphosphate binding / meiosis I / proteasome regulatory particle / cytosolic proteasome complex / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / negative regulation of programmed cell death / protein K63-linked deubiquitination / symbiont entry into host cell via disruption of host cell glycocalyx / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / proteasome core complex / Resolution of D-loop Structures through Holliday Junction Intermediates / Somitogenesis / K63-linked deubiquitinase activity / symbiont entry into host cell via disruption of host cell envelope / Impaired BRCA2 binding to RAD51 / virus tail / proteasome binding / transcription factor binding / regulation of protein catabolic process / myofibril / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / general transcription initiation factor binding / polyubiquitin modification-dependent protein binding / blastocyst development / protein deubiquitination / positive regulation of RNA polymerase II transcription preinitiation complex assembly / regulation of proteasomal protein catabolic process / NF-kappaB binding / proteasome endopeptidase complex / endopeptidase activator activity / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / mRNA export from nucleus / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / enzyme regulator activity / immune system process / inclusion body / ERAD pathway / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / proteasome complex / NIK-->noncanonical NF-kB signaling / SCF-beta-TrCP mediated degradation of Emi1 / proteolysis involved in protein catabolic process / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / TBP-class protein binding / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / sarcomere / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / double-strand break repair via homologous recombination / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
![]() | Mao YD | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome. Authors: Yuanchen Dong / Shuwen Zhang / Zhaolong Wu / Xuemei Li / Wei Li Wang / Yanan Zhu / Svetla Stoilova-McPhie / Ying Lu / Daniel Finley / Youdong Mao / ![]() ![]() Abstract: The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of ...The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of the substrate-engaged human proteasome in seven conformational states at 2.8-3.6 Å resolution, captured during breakdown of a polyubiquitylated protein. These structures illuminate a spatiotemporal continuum of dynamic substrate-proteasome interactions from ubiquitin recognition to substrate translocation, during which ATP hydrolysis sequentially navigates through all six ATPases. There are three principal modes of coordinated hydrolysis, featuring hydrolytic events in two oppositely positioned ATPases, in two adjacent ATPases and in one ATPase at a time. These hydrolytic modes regulate deubiquitylation, initiation of translocation and processive unfolding of substrates, respectively. Hydrolysis of ATP powers a hinge-like motion in each ATPase that regulates its substrate interaction. Synchronization of ATP binding, ADP release and ATP hydrolysis in three adjacent ATPases drives rigid-body rotations of substrate-bound ATPases that are propagated unidirectionally in the ATPase ring and unfold the substrate. | ||||||||||||
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 | ![]() | 748.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 68.9 KB 68.9 KB | Display Display | ![]() |
Images | ![]() | 37.6 KB | ||
Filedesc metadata | ![]() | 15.8 KB | ||
Others | ![]() ![]() | 731.4 MB 756.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 639.2 KB | Display | ![]() |
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Full document | ![]() | 638.8 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6msdMC ![]() 9215C ![]() 9216C ![]() 9218C ![]() 9219C ![]() 9220C ![]() 9221C ![]() 9222C ![]() 9223C ![]() 9224C ![]() 9225C ![]() 9226C ![]() 9227C ![]() 9228C ![]() 9229C ![]() 6msbC ![]() 6mseC ![]() 6msgC ![]() 6mshC ![]() 6msjC ![]() 6mskC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 13.9 TB Data #1: Drift-corrected frame-averaged super-counting mode micrographs and extracted particles of substrate-engaged human 26S proteasome [micrographs - single frame]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The complete map of state EA2 of substrate-engaged human proteasome, low pass-filtered to 3 Angstrom without amplitude correction. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.685 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unfiltered, uncorrected raw EA2 map of complete holoenzyme
File | emd_9217_additional_1.map | ||||||||||||
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Annotation | Unfiltered, uncorrected raw EA2 map of complete holoenzyme | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: The complete map of state EA2 of substrate-engaged...
File | emd_9217_additional_2.map | ||||||||||||
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Annotation | The complete map of state EA2 of substrate-engaged human proteasome, low pass-filtered to 3.2 Angstrom with amplitude correction with a B-factor of -46 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Human 26S proteasome
+Supramolecule #1: Human 26S proteasome
+Macromolecule #1: 26S proteasome non-ATPase regulatory subunit 1
+Macromolecule #2: 26S proteasome non-ATPase regulatory subunit 3
+Macromolecule #3: 26S proteasome non-ATPase regulatory subunit 12
+Macromolecule #4: 26S proteasome non-ATPase regulatory subunit 11
+Macromolecule #5: 26S proteasome non-ATPase regulatory subunit 6
+Macromolecule #6: 26S proteasome non-ATPase regulatory subunit 7
+Macromolecule #7: 26S proteasome non-ATPase regulatory subunit 13
+Macromolecule #8: 26S proteasome non-ATPase regulatory subunit 4
+Macromolecule #9: 26S proteasome non-ATPase regulatory subunit 14
+Macromolecule #10: 26S proteasome non-ATPase regulatory subunit 8
+Macromolecule #11: 26S proteasome complex subunit SEM1
+Macromolecule #12: 26S proteasome non-ATPase regulatory subunit 2
+Macromolecule #13: 26S proteasome regulatory subunit 7
+Macromolecule #14: 26S proteasome regulatory subunit 4
+Macromolecule #15: 26S proteasome regulatory subunit 8
+Macromolecule #16: 26S proteasome regulatory subunit 6B
+Macromolecule #17: 26S proteasome regulatory subunit 10B
+Macromolecule #18: 26S proteasome regulatory subunit 6A
+Macromolecule #19: Ubiquitin
+Macromolecule #20: Proteasome subunit alpha type-6
+Macromolecule #21: Proteasome subunit alpha type-2
+Macromolecule #22: Proteasome subunit alpha type-4
+Macromolecule #23: Proteasome subunit alpha type-7
+Macromolecule #24: Proteasome subunit alpha type-5
+Macromolecule #25: Proteasome subunit alpha type-1
+Macromolecule #26: Proteasome subunit alpha type-3
+Macromolecule #27: Proteasome subunit beta type-6
+Macromolecule #28: Proteasome subunit beta type-7
+Macromolecule #29: Proteasome subunit beta type-3
+Macromolecule #30: Proteasome subunit beta type-2
+Macromolecule #31: Proteasome subunit beta type-5
+Macromolecule #32: Proteasome subunit beta type-1
+Macromolecule #33: Proteasome subunit beta type-4
+Macromolecule #34: ZINC ION
+Macromolecule #35: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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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) / Average electron dose: 44.0 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 |