5T0C

Structural basis for dynamic regulation of the human 26S proteasome

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

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 U S A 113: 12991-12996

  • DOI: 10.1073/pnas.1614614113
  • Primary Citation of Related Structures:  
    5T0C, 5T0G, 5T0H, 5T0I, 5T0J

  • 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 that are concurrently translocated into a proteolytic chamber and degraded into peptides ...

    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: 

    Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1A [auth AU],
GA [auth BU]		953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
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GTEx:  ENSG00000173692 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3B [auth AV],
HA [auth BV]		533Homo sapiensMutation(s): 0 
Gene Names: PSMD3
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GTEx:  ENSG00000108344 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12C [auth AW],
IA [auth BW]		456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
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GTEx:  ENSG00000197170 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11D [auth AX],
JA [auth BX]		422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6E [auth AY],
KA [auth BY]		389Homo sapiensMutation(s): 0 
Gene Names: PSMD6, KIAA0107, PFAAP4
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7F [auth AZ],
LA [auth BZ]		324Homo sapiensMutation(s): 0 
Gene Names: PSMD7, MOV34L
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13G [auth Aa],
MA [auth Ba]		376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4H [auth Ab],
NA [auth Bb]		377Homo sapiensMutation(s): 0 
Gene Names: PSMD4, MCB1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14I [auth Ac],
OA [auth Bc]		310Homo sapiensMutation(s): 0 
Gene Names: PSMD14, POH1
EC: 3.4.19
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8J [auth Ad],
PA [auth Bd]		257Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome complex subunit DSS1K [auth Ae],
QA [auth Be]		70Homo sapiensMutation(s): 0 
Gene Names: SEM1, C7orf76, DSS1, SHFDG1, SHFM1
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GTEx:  ENSG00000127922 
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Entity ID: 12
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26S proteasome non-ATPase regulatory subunit 2L [auth Af],
RA [auth Bf]		908Homo sapiensMutation(s): 0 
Gene Names: PSMD2, TRAP2
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GTEx:  ENSG00000175166 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 7M [auth AA],
SA [auth BA]		433Homo sapiensMutation(s): 0 
Gene Names: PSMC2, MSS1
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GTEx:  ENSG00000161057 
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Entity ID: 14
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26S protease regulatory subunit 4N [auth AB],
TA [auth BB]		440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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GTEx:  ENSG00000100764 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 6BO [auth AD],
UA [auth BD]		418Homo sapiensMutation(s): 0 
Gene Names: PSMC4, MIP224, TBP7
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 10BP [auth AE],
VA [auth BE]		389Homo sapiensMutation(s): 0 
Gene Names: PSMC6, SUG2
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 6AQ [auth AF],
WA [auth BF]		439Homo sapiensMutation(s): 0 
Gene Names: PSMC3, TBP1
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
26S protease regulatory subunit 8R [auth AC],
XA [auth BC]		406Homo sapiensMutation(s): 0 
Gene Names: PSMC5, SUG1
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GTEx:  ENSG00000087191 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6S [auth AG],
YA [auth BG]		245Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2T [auth AH],
ZA [auth BH]		233Homo sapiensMutation(s): 0 
Gene Names: PSMA2, HC3, PSC3
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4U [auth AI],
AB [auth BI]		260Homo sapiensMutation(s): 0 
Gene Names: PSMA4, HC9, PSC9
EC: 3.4.25.1
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GTEx:  ENSG00000041357 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7V [auth AJ],
BB [auth BJ]		247Homo sapiensMutation(s): 0 
Gene Names: PSMA7, HSPC
EC: 3.4.25.1
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GTEx:  ENSG00000101182 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5W [auth AK],
CB [auth BK]		240Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1X [auth AL],
DB [auth BL]		268Homo sapiensMutation(s): 0 
Gene Names: PSMA1, HC2, NU, PROS30, PSC2
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3Y [auth AM],
EB [auth BM]		254Homo sapiensMutation(s): 0 
Gene Names: PSMA3, HC8, PSC8
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6Z [auth AN],
FB [auth BN]		238Homo sapiensMutation(s): 0 
Gene Names: PSMB6, LMPY, Y
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7AA [auth AO],
GB [auth BO]		276Homo sapiensMutation(s): 0 
Gene Names: PSMB7, Z
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3BA [auth AP],
HB [auth BP]		204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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GTEx:  ENSG00000277791 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2CA [auth AQ],
IB [auth BQ]		201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5DA [auth AR],
JB [auth BR]		262Homo sapiensMutation(s): 0 
Gene Names: PSMB5, LMPX, MB1, X
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1EA [auth AS],
KB [auth BS]		240Homo sapiensMutation(s): 0 
Gene Names: PSMB1, PSC5
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4FA [auth AT],
LB [auth BT]		263Homo sapiensMutation(s): 0 
Gene Names: PSMB4, PROS26
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
NB [auth AA],
PB [auth AD],
QB [auth AE],
RB [auth AF],
UB [auth BA],
NB [auth AA],
PB [auth AD],
QB [auth AE],
RB [auth AF],
UB [auth BA],
WB [auth BD],
XB [auth BE],
YB [auth BF]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
ADP
Query on ADP
Download Ideal Coordinates CCD File 
OB [auth AB],
SB [auth AC],
VB [auth BB],
ZB [auth BC]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
MB [auth Ac],
TB [auth Bc]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-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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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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