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: 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) ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2AO234Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4BP261Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7C234Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
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PHAROS  O14818
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5DR241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
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PHAROS  P28066
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1E234Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3FT255Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6GU246Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7HV277Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3IW205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2JX196Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5KY204Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
Find proteins for P28074 (Homo sapiens)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1LZ241Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4Ma264Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6Nb239Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7Q235Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1S238Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 7c433Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
Find proteins for P35998 (Homo sapiens)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 4d428Homo sapiensMutation(s): 0 
Gene Names: PSMC1
Find proteins for P62191 (Homo sapiens)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 6Be418Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
Find proteins for P43686 (Homo sapiens)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 10Bf379Homo sapiensMutation(s): 0 
Gene Names: PSMC6SUG2
Find proteins for P62333 (Homo sapiens)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 6Ag439Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
Find proteins for P17980 (Homo sapiens)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 8h355Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
Find proteins for P62195 (Homo sapiens)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1i953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
Find proteins for Q99460 (Homo sapiens)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3j534Homo sapiensMutation(s): 0 
Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12k456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
Find proteins for O00232 (Homo sapiens)
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PHAROS  O00232
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11l422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
Find proteins for O00231 (Homo sapiens)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6m389Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
Find proteins for Q15008 (Homo sapiens)
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PHAROS  Q15008
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7n324Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
Find proteins for P51665 (Homo sapiens)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13o376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
Find proteins for Q9UNM6 (Homo sapiens)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4p377Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
Find proteins for P55036 (Homo sapiens)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14q310Homo sapiensMutation(s): 0 
Gene Names: PSMD14POH1
EC: 3.4.19
Find proteins for O00487 (Homo sapiens)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8r350Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1s70Homo sapiensMutation(s): 0 
Gene Names: SEM1C7orf76DSS1SHFDG1SHFM1
Find proteins for P60896 (Homo sapiens)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
bound Oprozomibtu4synthetic constructMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
c, d, e, g, h
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

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 

  • 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