5M32

Human 26S proteasome in complex with Oprozomib


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
A, O
234Homo sapiensMutation(s): 0 
Gene Names: PSMA2 (HC3, PSC3)
EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens)
Go to Gene View: PSMA2
Go to UniProtKB:  P25787
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
B, P
261Homo sapiensMutation(s): 0 
Gene Names: PSMA4 (HC9, PSC9)
EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens)
Go to Gene View: PSMA4
Go to UniProtKB:  P25789
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-7
C
234Homo sapiensMutation(s): 0 
Gene Names: PSMA7 (HSPC)
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
Go to Gene View: PSMA7
Go to UniProtKB:  O14818
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
D, R
241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
Go to Gene View: PSMA5
Go to UniProtKB:  P28066
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
E
234Homo sapiensMutation(s): 0 
Gene Names: PSMA1 (HC2, NU, PROS30, PSC2)
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
Go to Gene View: PSMA1
Go to UniProtKB:  P25786
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
F, T
255Homo sapiensMutation(s): 0 
Gene Names: PSMA3 (HC8, PSC8)
EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens)
Go to Gene View: PSMA3
Go to UniProtKB:  P25788
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
G, U
246Homo sapiensMutation(s): 0 
Gene Names: PSMA6 (PROS27)
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
Go to Gene View: PSMA6
Go to UniProtKB:  P60900
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
H, V
277Homo sapiensMutation(s): 0 
Gene Names: PSMB7 (Z)
EC: 3.4.25.1
Find proteins for Q99436 (Homo sapiens)
Go to Gene View: PSMB7
Go to UniProtKB:  Q99436
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
I, W
205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
Go to Gene View: PSMB3
Go to UniProtKB:  P49720
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
J, X
196Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
Find proteins for P49721 (Homo sapiens)
Go to Gene View: PSMB2
Go to UniProtKB:  P49721
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
K, Y
204Homo sapiensMutation(s): 0 
Gene Names: PSMB5 (LMPX, MB1, X)
EC: 3.4.25.1
Find proteins for P28074 (Homo sapiens)
Go to Gene View: PSMB5
Go to UniProtKB:  P28074
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
L, Z
241Homo sapiensMutation(s): 0 
Gene Names: PSMB1 (PSC5)
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
Go to Gene View: PSMB1
Go to UniProtKB:  P20618
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
M, a
264Homo sapiensMutation(s): 0 
Gene Names: PSMB4 (PROS26)
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
Go to Gene View: PSMB4
Go to UniProtKB:  P28070
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
N, b
239Homo sapiensMutation(s): 0 
Gene Names: PSMB6 (LMPY, Y)
EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens)
Go to Gene View: PSMB6
Go to UniProtKB:  P28072
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-7
Q
235Homo sapiensMutation(s): 0 
Gene Names: PSMA7 (HSPC)
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
Go to Gene View: PSMA7
Go to UniProtKB:  O14818
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
S
238Homo sapiensMutation(s): 0 
Gene Names: PSMA1 (HC2, NU, PROS30, PSC2)
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
Go to Gene View: PSMA1
Go to UniProtKB:  P25786
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 7
c
433Homo sapiensMutation(s): 0 
Gene Names: PSMC2 (MSS1)
Find proteins for P35998 (Homo sapiens)
Go to Gene View: PSMC2
Go to UniProtKB:  P35998
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 4
d
428Homo sapiensMutation(s): 0 
Gene Names: PSMC1
Find proteins for P62191 (Homo sapiens)
Go to Gene View: PSMC1
Go to UniProtKB:  P62191
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 6B
e
418Homo sapiensMutation(s): 0 
Gene Names: PSMC4 (MIP224, TBP7)
Find proteins for P43686 (Homo sapiens)
Go to Gene View: PSMC4
Go to UniProtKB:  P43686
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 10B
f
379Homo sapiensMutation(s): 0 
Gene Names: PSMC6 (SUG2)
Find proteins for P62333 (Homo sapiens)
Go to Gene View: PSMC6
Go to UniProtKB:  P62333
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 6A
g
439Homo sapiensMutation(s): 0 
Gene Names: PSMC3 (TBP1)
Find proteins for P17980 (Homo sapiens)
Go to Gene View: PSMC3
Go to UniProtKB:  P17980
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 8
h
355Homo sapiensMutation(s): 0 
Gene Names: PSMC5 (SUG1)
Find proteins for P62195 (Homo sapiens)
Go to Gene View: PSMC5
Go to UniProtKB:  P62195
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 1
i
953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
Find proteins for Q99460 (Homo sapiens)
Go to Gene View: PSMD1
Go to UniProtKB:  Q99460
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 3
j
534Homo sapiensMutation(s): 0 
Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens)
Go to Gene View: PSMD3
Go to UniProtKB:  O43242
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 12
k
456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
Find proteins for O00232 (Homo sapiens)
Go to Gene View: PSMD12
Go to UniProtKB:  O00232
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 11
l
422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
Find proteins for O00231 (Homo sapiens)
Go to Gene View: PSMD11
Go to UniProtKB:  O00231
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 6
m
389Homo sapiensMutation(s): 0 
Gene Names: PSMD6 (KIAA0107, PFAAP4)
Find proteins for Q15008 (Homo sapiens)
Go to Gene View: PSMD6
Go to UniProtKB:  Q15008
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 7
n
324Homo sapiensMutation(s): 0 
Gene Names: PSMD7 (MOV34L)
Find proteins for P51665 (Homo sapiens)
Go to Gene View: PSMD7
Go to UniProtKB:  P51665
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 13
o
376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
Find proteins for Q9UNM6 (Homo sapiens)
Go to Gene View: PSMD13
Go to UniProtKB:  Q9UNM6
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 4
p
377Homo sapiensMutation(s): 0 
Gene Names: PSMD4 (MCB1)
Find proteins for P55036 (Homo sapiens)
Go to Gene View: PSMD4
Go to UniProtKB:  P55036
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 14
q
310Homo sapiensMutation(s): 0 
Gene Names: PSMD14 (POH1)
EC: 3.4.19.-
Find proteins for O00487 (Homo sapiens)
Go to Gene View: PSMD14
Go to UniProtKB:  O00487
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 8
r
350Homo sapiensMutation(s): 0 
Gene Names: PSMD8
Find proteins for P48556 (Homo sapiens)
Go to Gene View: PSMD8
Go to UniProtKB:  P48556
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
26S proteasome complex subunit SEM1
s
70Homo sapiensMutation(s): 0 
Gene Names: SEM1 (C7orf76, DSS1, SHFDG1, SHFM1)
Find proteins for P60896 (Homo sapiens)
Go to Gene View: SEM1
Go to UniProtKB:  P60896
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
bound Oprozomib
t, u
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
c, d, e, g, h
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
6V9
Query on 6V9
t, u
peptide linkingC5 H5 N O2 S

--

6VA
Query on 6VA
t, u
NON-POLYMERC12 H19 N O2

--

7C9
Query on 7C9
t, u
L-peptide linkingC4 H9 N O3

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection