5VHI

Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.8 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

Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle.

Lu, Y.Wu, J.Dong, Y.Chen, S.Sun, S.Ma, Y.B.Ouyang, Q.Finley, D.Kirschner, M.W.Mao, Y.

(2017) Mol. Cell 67: 322-333.e6

  • DOI: 10.1016/j.molcel.2017.06.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP a ...

    The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP assembly chaperones in mammals: PAAF1, p28/gankyrin, p27/PSMD9, and S5b. Using cryogenic electron microscopy, we analyzed the non-AAA structure of the p28-bound human RP at 4.5 Å resolution and determined seven distinct conformations of the Rpn1-p28-AAA subcomplex within the p28-bound RP at subnanometer resolutions. Remarkably, the p28-bound AAA ring does not form a channel in the free RP and spontaneously samples multiple "open" and "closed" topologies at the Rpt2-Rpt6 and Rpt3-Rpt4 interfaces. Our analysis suggests that p28 assists the proteolytic core particle to select a specific conformation of the ATPase ring for RP engagement and is released in a shoehorn-like fashion in the last step of the chaperone-mediated proteasome assembly.


    Organizational Affiliation

    State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China.,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: marc@hms.harvard.edu.,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China; Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: youdong_mao@dfci.harvard.edu.,Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China; Peking-Tsinghua Joint Center for Life Science, Peking University, Beijing 100871, China.,Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 7
A
352Homo sapiensMutation(s): 0 
Gene Names: PSMC2 (MSS1)
Find proteins for P35998 (Homo sapiens)
Go to Gene View: PSMC2
Go to UniProtKB:  P35998
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 4
B
341Homo sapiensMutation(s): 0 
Gene Names: PSMC1
Find proteins for P62191 (Homo sapiens)
Go to Gene View: PSMC1
Go to UniProtKB:  P62191
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 8
C
385Homo sapiensMutation(s): 0 
Gene Names: PSMC5 (SUG1)
Find proteins for P62195 (Homo sapiens)
Go to Gene View: PSMC5
Go to UniProtKB:  P62195
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 6B
D
368Homo 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: 5
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 10B
E
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: 6
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 6A
F
380Homo sapiensMutation(s): 0 
Gene Names: PSMC3 (TBP1)
Find proteins for P17980 (Homo sapiens)
Go to Gene View: PSMC3
Go to UniProtKB:  P17980
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 1
U
935Homo sapiensMutation(s): 0 
Gene Names: PSMD1
Find proteins for Q99460 (Homo sapiens)
Go to Gene View: PSMD1
Go to UniProtKB:  Q99460
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 3
V
488Homo sapiensMutation(s): 0 
Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens)
Go to Gene View: PSMD3
Go to UniProtKB:  O43242
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 12
W
456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
Find proteins for O00232 (Homo sapiens)
Go to Gene View: PSMD12
Go to UniProtKB:  O00232
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 11
X
385Homo sapiensMutation(s): 0 
Gene Names: PSMD11
Find proteins for O00231 (Homo sapiens)
Go to Gene View: PSMD11
Go to UniProtKB:  O00231
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 6
Y
378Homo 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: 12
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 7
Z
286Homo sapiensMutation(s): 0 
Gene Names: PSMD7 (MOV34L)
Find proteins for P51665 (Homo sapiens)
Go to Gene View: PSMD7
Go to UniProtKB:  P51665
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 13
a
374Homo sapiensMutation(s): 0 
Gene Names: PSMD13
Find proteins for Q9UNM6 (Homo sapiens)
Go to Gene View: PSMD13
Go to UniProtKB:  Q9UNM6
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 4
b
191Homo sapiensMutation(s): 0 
Gene Names: PSMD4 (MCB1)
Find proteins for P55036 (Homo sapiens)
Go to Gene View: PSMD4
Go to UniProtKB:  P55036
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 14
c
287Homo 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: 16
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 8
d
257Homo sapiensMutation(s): 0 
Gene Names: PSMD8
Find proteins for P48556 (Homo sapiens)
Go to Gene View: PSMD8
Go to UniProtKB:  P48556
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 10
G
226Homo sapiensMutation(s): 0 
Gene Names: PSMD10
Find proteins for O75832 (Homo sapiens)
Go to Gene View: PSMD10
Go to UniProtKB:  O75832
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
26S proteasome complex subunit SEM1
e
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: 19
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 2
f
848Homo sapiensMutation(s): 0 
Gene Names: PSMD2 (TRAP2)
Find proteins for Q13200 (Homo sapiens)
Go to Gene View: PSMD2
Go to UniProtKB:  Q13200
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
c
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2018-08-22
    Type: Data collection, Database references