5GJQ

Structure of the human 26S proteasome bound to USP14-UbAl


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.35 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

An atomic structure of the human 26S proteasome.

Huang, X.Luan, B.Wu, J.Shi, Y.

(2016) Nat Struct Mol Biol 23: 778-785

  • DOI: https://doi.org/10.1038/nsmb.3273
  • Primary Citation of Related Structures:  
    5GJQ, 5GJR

  • PubMed Abstract: 

    We report the cryo-EM structure of the human 26S proteasome at an average resolution of 3.5 Å, allowing atomic modeling of 28 subunits in the core particle (CP) and 18 subunits in the regulatory particle (RP). The C-terminal residues of Rpt3 and Rpt5 subunits in the RP can be seen inserted into surface pockets formed between adjacent α subunits in the CP. Each of the six Rpt subunits contains a bound nucleotide, and the central gate of the CP α-ring is closed despite RP association. The six pore 1 loops in the Rpt ring are arranged similarly to a spiral staircase along the axial channel of substrate transport, which is constricted by the pore 2 loops. We also determined the cryo-EM structure of the human proteasome bound to the deubiquitinating enzyme USP14 at 4.35-Å resolution. Together, our structures provide a framework for mechanistic understanding of eukaryotic proteasome function.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6A [auth a],
CA [auth o]
239Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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UniProt GroupP28072
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6B,
O [auth h]
246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7C [auth b],
EA [auth p]
277Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2D [auth C],
Q [auth i]
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3E [auth c],
GA [auth q]
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000277791 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4F [auth D],
S [auth j]
261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000041357 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2G [auth d],
IA [auth r]
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7H [auth E],
U [auth k]
248Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000101182 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5I [auth e],
KA [auth s]
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5J [auth F],
W [auth l]
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1K [auth f],
MA [auth t]
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1L [auth G],
Y [auth m]
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4M [auth g],
OA [auth u]
264Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 7N [auth H]433Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161057 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 4P [auth I]440Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100764 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 8R [auth J]406Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087191 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 6BT [auth K]418Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000013275 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 10BV [auth L]389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100519 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 6AX [auth M]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165916 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1Z [auth N]953Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173692 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3AA [auth n],
RA [auth X]
255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13BA [auth O]376Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185627 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12DA [auth P]456Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197170 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11FA [auth Q]422Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108671 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6HA [auth R]389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163636 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3JA [auth S]534Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108344 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8LA [auth T]350Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099341 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7NA [auth U]324Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000103035 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14PA [auth V]310Homo sapiensMutation(s): 0 
EC: 3.4.19
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GTEx:  ENSG00000115233 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4QA [auth W]377Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159352 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit DSS1SA [auth Y]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000127922 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2TA [auth Z]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175166 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 14UA [auth x]494Homo sapiensMutation(s): 0 
Gene Names: USP14TGT
EC: 3.4.19.12
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GTEx:  ENSG00000101557 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-BVA [auth y]76Homo sapiensMutation(s): 0 
Gene Names: UBB
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GTEx:  ENSG00000170315 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC4.5
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31130002
National Natural Science Foundation of ChinaChina31321062
National Natural Science Foundation of ChinaChina31430020

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.2: 2018-10-24
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-11-06
    Changes: Advisory, Data collection, Derived calculations, Other