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: https://doi.org/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. 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 Systems Biology, Harvard Medical School, Boston, MA 02115; marc@hms.harvard.edu youdong_mao@dfci.harvard.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1A [auth AU],
GA [auth BU]
953Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173692 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3B [auth AV],
HA [auth BV]
533Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108344 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12C [auth AW],
IA [auth BW]
456Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197170 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11D [auth AX],
JA [auth BX]
422Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108671 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6E [auth AY],
KA [auth BY]
389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163636 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7F [auth AZ],
LA [auth BZ]
324Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000103035 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13G [auth Aa],
MA [auth Ba]
376Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185627 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4H [auth Ab],
NA [auth Bb]
377Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159352 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14I [auth Ac],
OA [auth Bc]
310Homo sapiensMutation(s): 0 
EC: 3.4.19
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GTEx:  ENSG00000115233 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8J [auth Ad],
PA [auth Bd]
257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099341 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit DSS1K [auth Ae],
QA [auth Be]
70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000127922 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2L [auth Af],
RA [auth Bf]
908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175166 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 7M [auth AA],
SA [auth BA]
433Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161057 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 4N [auth AB],
TA [auth BB]
440Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100764 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 6BO [auth AD],
UA [auth BD]
418Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000013275 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 10BP [auth AE],
VA [auth BE]
389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100519 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 6AQ [auth AF],
WA [auth BF]
439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165916 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 8R [auth AC],
XA [auth BC]
406Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087191 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6S [auth AG],
YA [auth BG]
245Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2T [auth AH],
ZA [auth BH]
233Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4AB [auth BI],
U [auth AI]
260Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000041357 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7BB [auth BJ],
V [auth AJ]
247Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000101182 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5CB [auth BK],
W [auth AK]
240Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1DB [auth BL],
X [auth AL]
268Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3EB [auth BM],
Y [auth AM]
254Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6FB [auth BN],
Z [auth AN]
238Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7AA [auth AO],
GB [auth BO]
276Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3BA [auth AP],
HB [auth BP]
204Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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PHAROS:  P49720
GTEx:  ENSG00000277791 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2CA [auth AQ],
IB [auth BQ]
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5DA [auth AR],
JB [auth BR]
262Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1EA [auth AS],
KB [auth BS]
240Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4FA [auth AT],
LB [auth BT]
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Small Molecules
Ligands 3 Unique
IDChains Name / 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
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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
MB [auth Ac],
TB [auth Bc]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.3
MODEL REFINEMENTPHENIX10

Structure Validation

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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