5M32

Human 26S proteasome in complex with Oprozomib


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Long-range allosteric regulation of the human 26S proteasome by 20S proteasome-targeting cancer drugs.

Haselbach, D.Schrader, J.Lambrecht, F.Henneberg, F.Chari, A.Stark, H.

(2017) Nat Commun 8: 15578-15578

  • DOI: https://doi.org/10.1038/ncomms15578
  • Primary Citation of Related Structures:  
    5M32

  • PubMed 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 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.


  • Organizational Affiliation

    Department for Structural Dynamics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2
A, O
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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UniProt GroupP25787
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
B, P
261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P25789 (Homo sapiens)
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GTEx:  ENSG00000041357 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000101182 
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UniProt GroupO14818
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
D, R
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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UniProt GroupP25786
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
F, T
255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
G, U
246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7
H, V
277Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
I, W
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000277791 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2
J, X
196Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5
K, Y
204Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1
L, Z
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4AA [auth a],
M
264Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6BA [auth b],
N
239Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7235Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for O14818 (Homo sapiens)
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GTEx:  ENSG00000101182 
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UniProt GroupO14818
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1238Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 7CA [auth c]433Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161057 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 4DA [auth d]428Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100764 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 6BEA [auth e]418Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000013275 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 10BFA [auth f]379Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100519 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 6AGA [auth g]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165916 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 8HA [auth h]355Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087191 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1IA [auth i]953Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173692 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3JA [auth j]534Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108344 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12KA [auth k]456Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197170 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11LA [auth l]422Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108671 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6MA [auth m]389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163636 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7NA [auth n]324Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000103035 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13OA [auth o]376Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185627 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4PA [auth p]377Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159352 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14QA [auth q]310Homo sapiensMutation(s): 0 
EC: 3.4.19
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GTEx:  ENSG00000115233 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8RA [auth r]350Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099341 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1SA [auth s]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000127922 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
bound OprozomibTA [auth t],
UA [auth u]
4synthetic constructMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyCH1098-1/1
German Research FoundationGermanySFB860-TP A5
ESFRIGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection
  • Version 1.2: 2019-10-09
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 1.3: 2019-12-11
    Changes: Other