5T0C

Structural basis for dynamic regulation of the human 26S proteasome

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 1.3 of the entry. See complete history. 

Literature

Structural basis for dynamic regulation of the human 26S proteasome.

Chen, S., Wu, J., Lu, Y., Ma, Y.B., Lee, B.H., Yu, Z., Ouyang, Q., Finley, D.J., Kirschner, M.W., Mao, Y.

(2016) Proc.Natl.Acad.Sci.USA 113: 12991-12996

  • DOI: 10.1073/pnas.1614614113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The proteasome is the major engine of protein degradation in all eukaryotic cells. At the heart of this machine is a heterohexameric ring of AAA (ATPases associated with diverse cellular activities) proteins that unfolds ubiquitylated target proteins ...

    The proteasome is the major engine of protein degradation in all eukaryotic cells. At the heart of this machine is a heterohexameric ring of AAA (ATPases associated with diverse cellular activities) proteins that unfolds ubiquitylated target proteins that are concurrently translocated into a proteolytic chamber and degraded into peptides. Using cryoelectron microscopy, we determined a near-atomic-resolution structure of the 2.5-MDa human proteasome in its ground state, as well as subnanometer-resolution structures of the holoenzyme in three alternative conformational states. The substrate-unfolding AAA-ATPase channel is narrowed by 10 inward-facing pore loops arranged into two helices that run in parallel with each other, one hydrophobic in character and the other highly charged. The gate of the core particle was unexpectedly found closed in the ground state and open in only one of the alternative states. Coordinated, stepwise conformational changes of the regulatory particle couple ATP hydrolysis to substrate translocation and regulate gating of the core particle, leading to processive degradation.

    Organizational Affiliation: 

    Center for Quantitative Biology, Peking University, Beijing 100871, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 1
AU, BU
953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
Find proteins for Q99460 (Homo sapiens)
Go to Gene View: PSMD1
Go to UniProtKB:  Q99460
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 3
AV, BV
533Homo sapiensMutation(s): 0 
Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens)
Go to Gene View: PSMD3
Go to UniProtKB:  O43242
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 12
AW, BW
456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
Find proteins for O00232 (Homo sapiens)
Go to Gene View: PSMD12
Go to UniProtKB:  O00232
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 11
AX, BX
422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
Find proteins for O00231 (Homo sapiens)
Go to Gene View: PSMD11
Go to UniProtKB:  O00231
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 6
AY, BY
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: 6
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 7
AZ, BZ
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: 7
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 13
Aa, Ba
376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
Find proteins for Q9UNM6 (Homo sapiens)
Go to Gene View: PSMD13
Go to UniProtKB:  Q9UNM6
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 4
Ab, Bb
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: 9
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 14
Ac, Bc
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: 10
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 8
Ad, Bd
257Homo sapiensMutation(s): 0 
Gene Names: PSMD8
Find proteins for P48556 (Homo sapiens)
Go to Gene View: PSMD8
Go to UniProtKB:  P48556
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
26S proteasome complex subunit DSS1
Ae, Be
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: 12
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 2
Af, Bf
908Homo sapiensMutation(s): 0 
Gene Names: PSMD2 (TRAP2)
Find proteins for Q13200 (Homo sapiens)
Go to Gene View: PSMD2
Go to UniProtKB:  Q13200
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 7
AA, BA
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: 14
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 4
AB, BB
440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
Find proteins for P62191 (Homo sapiens)
Go to Gene View: PSMC1
Go to UniProtKB:  P62191
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 6B
AD, BD
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: 16
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 10B
AE, BE
389Homo sapiensMutation(s): 0 
Gene Names: PSMC6 (SUG2)
Find proteins for P62333 (Homo sapiens)
Go to Gene View: PSMC6
Go to UniProtKB:  P62333
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 6A
AF, BF
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: 18
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 8
AC, BC
406Homo sapiensMutation(s): 0 
Gene Names: PSMC5 (SUG1)
Find proteins for P62195 (Homo sapiens)
Go to Gene View: PSMC5
Go to UniProtKB:  P62195
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
AG, BG
245Homo 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: 20
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
AH, BH
233Homo 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: 21
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
AI, BI
260Homo 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: 22
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-7
AJ, BJ
247Homo 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: 23
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
AK, BK
240Homo 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: 24
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
AL, BL
268Homo 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: 25
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
AM, BM
254Homo 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: 26
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
AN, BN
238Homo 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: 27
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
AO, BO
276Homo 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: 28
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
AP, BP
204Homo 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: 29
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
AQ, BQ
201Homo 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: 30
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
AR, BR
262Homo 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: 31
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
AS, BS
240Homo 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: 32
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
AT, BT
263Homo 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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download SDF File 
Download CCD File 
AA, AD, AE, AF, BA, BD, BE, BF
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
Ac, Bc
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP
Download SDF File 
Download CCD File 
AB, AC, BB, BC
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references
  • Version 1.2: 2016-11-30
    Type: Database references
  • Version 1.3: 2018-07-18
    Type: Data collection, Database references