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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4146 | ||||||||||||
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Title | Human 26S proteasome in complex with Oprozomib | ||||||||||||
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Function / homology | ![]() positive regulation of inclusion body assembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / integrator complex / purine ribonucleoside triphosphate binding / meiosis I ...positive regulation of inclusion body assembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / integrator 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 / 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 / Homologous DNA Pairing and Strand Exchange / Regulation of ornithine decarboxylase (ODC) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / proteasome core complex / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / K63-linked deubiquitinase activity / Impaired BRCA2 binding to RAD51 / immune system process / myofibril / proteasome binding / regulation of protein catabolic process / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / 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 / mRNA export from nucleus / 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 Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
![]() | Haselbach D / Schrader J / Lambrecht F / Henneberg F / Chari A / Stark H | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Long-range allosteric regulation of the human 26S proteasome by 20S proteasome-targeting cancer drugs. Authors: David Haselbach / Jil Schrader / Felix Lambrecht / Fabian Henneberg / Ashwin Chari / Holger Stark / ![]() Abstract: The proteasome holoenzyme is the major non-lysosomal protease; its proteolytic activity is essential for cellular homeostasis. Thus, it is an attractive target for the development of ...The proteasome holoenzyme is the major non-lysosomal protease; its proteolytic activity is essential for cellular homeostasis. Thus, it is an attractive target for the development of chemotherapeutics. While the structural basis of core particle (CP) inhibitors is largely understood, their structural impact on the proteasome holoenzyme remains entirely elusive. Here, we determined the structure of the 26S proteasome with and without the inhibitor Oprozomib. Drug binding modifies the energy landscape of conformational motion in the proteasome regulatory particle (RP). Structurally, the energy barrier created by Oprozomib triggers a long-range allosteric regulation, resulting in the stabilization of a non-productive state. Thereby, the chemical drug-binding signal is converted, propagated and amplified into structural changes over a distance of more than 150 Å from the proteolytic site to the ubiquitin receptor Rpn10. The direct visualization of changes in conformational dynamics upon drug binding allows new ways to screen and develop future allosteric proteasome inhibitors. | ||||||||||||
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 | ![]() | 13.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 56.6 KB 56.6 KB | Display Display | ![]() |
Images | ![]() | 150.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 232.9 KB | Display | ![]() |
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Full document | ![]() | 232 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m32MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 100.5 Data #1: Particle stack of aligned, summed and dose weighted particle images from the human 26S proteasome bound to oprozomib. [picked particles - single frame - processed]) |
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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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Voxel size | X=Y=Z: 1.27 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 : human 26S proteasome in complex with oprozomib
+Supramolecule #1: human 26S proteasome in complex with oprozomib
+Supramolecule #2: human 26S proteasome
+Supramolecule #3: bound oprozomib
+Macromolecule #1: Proteasome subunit alpha type-2
+Macromolecule #2: Proteasome subunit alpha type-4
+Macromolecule #3: Proteasome subunit alpha type-7
+Macromolecule #4: Proteasome subunit alpha type-5
+Macromolecule #5: Proteasome subunit alpha type-1
+Macromolecule #6: Proteasome subunit alpha type-3
+Macromolecule #7: Proteasome subunit alpha type-6
+Macromolecule #8: Proteasome subunit beta type-7
+Macromolecule #9: Proteasome subunit beta type-3
+Macromolecule #10: Proteasome subunit beta type-2
+Macromolecule #11: Proteasome subunit beta type-5
+Macromolecule #12: Proteasome subunit beta type-1
+Macromolecule #13: Proteasome subunit beta type-4
+Macromolecule #14: Proteasome subunit beta type-6
+Macromolecule #15: Proteasome subunit alpha type-7
+Macromolecule #16: Proteasome subunit alpha type-1
+Macromolecule #17: 26S protease regulatory subunit 7
+Macromolecule #18: 26S protease regulatory subunit 4
+Macromolecule #19: 26S protease regulatory subunit 6B
+Macromolecule #20: 26S protease regulatory subunit 10B
+Macromolecule #21: 26S protease regulatory subunit 6A
+Macromolecule #22: 26S protease regulatory subunit 8
+Macromolecule #23: 26S proteasome non-ATPase regulatory subunit 1
+Macromolecule #24: 26S proteasome non-ATPase regulatory subunit 3
+Macromolecule #25: 26S proteasome non-ATPase regulatory subunit 12
+Macromolecule #26: 26S proteasome non-ATPase regulatory subunit 11
+Macromolecule #27: 26S proteasome non-ATPase regulatory subunit 6
+Macromolecule #28: 26S proteasome non-ATPase regulatory subunit 7
+Macromolecule #29: 26S proteasome non-ATPase regulatory subunit 13
+Macromolecule #30: 26S proteasome non-ATPase regulatory subunit 4
+Macromolecule #31: 26S proteasome non-ATPase regulatory subunit 14
+Macromolecule #32: 26S proteasome non-ATPase regulatory subunit 8
+Macromolecule #33: 26S proteasome complex subunit SEM1
+Macromolecule #34: bound Oprozomib
+Macromolecule #35: 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: 6.5 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 72 % / Chamber temperature: 4 K / Instrument: LEICA EM GP / Details: blot with sensor. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Microscope is equipped with Cs corrector |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 110236 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.0001 mm / Nominal defocus max: 8.4 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |