6WJN

SD-like state of human 26S Proteasome with non-cleavable M1-linked hexaubiquitin and E3 ubiquitin ligase E6AP/UBE3A

  • Classification: HYDROLASE/PROTEIN BINDING
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2020-04-14 Released: 2020-08-05 
  • Deposition Author(s): Chen, X., Walters, K.J.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Cryo-EM Reveals Unanchored M1-Ubiquitin Chain Binding at hRpn11 of the 26S Proteasome.

Chen, X., Dorris, Z., Shi, D., Huang, R.K., Khant, H., Fox, T., de Val, N., Williams, D., Zhang, P., Walters, K.J.

(2020) Structure 28: 1206-1217.e4

  • DOI: 10.1016/j.str.2020.07.011
  • Primary Citation of Related Structures:  
    6WJD, 6WJN

  • PubMed Abstract: 

    • The 26S proteasome is specialized for regulated protein degradation and formed by a dynamic regulatory particle (RP) that caps a hollow cylindrical core particle (CP) where substrates are proteolyzed. Its diverse substrates unify as proteasome targets by ubiquitination ...

    The 26S proteasome is specialized for regulated protein degradation and formed by a dynamic regulatory particle (RP) that caps a hollow cylindrical core particle (CP) where substrates are proteolyzed. Its diverse substrates unify as proteasome targets by ubiquitination. We used cryogenic electron microscopy (cryo-EM) to study how human 26S proteasome interacts with M1-linked hexaubiquitin (M1-Ub 6 ) unanchored to a substrate and E3 ubiquitin ligase E6AP/UBE3A. Proteasome structures are available with model substrates extending through the RP ATPase ring and substrate-conjugated K63-linked ubiquitin chains present at inhibited deubiquitinating enzyme hRpn11 and the nearby ATPase hRpt4/hRpt5 coiled coil. In this study, we find M1-Ub 6 at the hRpn11 site despite the absence of conjugated substrate, indicating that ubiquitin binding at this location does not require substrate interaction with the RP. Moreover, unanchored M1-Ub 6 binds to this hRpn11 site of the proteasome with the CP gating residues in both the closed and opened conformational states.

    Organizational Affiliation: 

    Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Electronic address: kylie.walters@nih.gov.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1A [auth U]911Homo sapiensMutation(s): 0 
Gene Names: PSMD1
Find proteins for Q99460 (Homo sapiens)
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GTEx:  ENSG00000173692
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3B [auth V]480Homo sapiensMutation(s): 0 
Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens)
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GTEx:  ENSG00000108344
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12C [auth W]456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
Find proteins for O00232 (Homo sapiens)
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GTEx:  ENSG00000197170
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11D [auth X]380Homo sapiensMutation(s): 0 
Gene Names: PSMD11
Find proteins for O00231 (Homo sapiens)
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GTEx:  ENSG00000108671
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6E [auth Y]378Homo sapiensMutation(s): 0 
Gene Names: PSMD6, KIAA0107, PFAAP4
Find proteins for Q15008 (Homo sapiens)
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GTEx:  ENSG00000163636
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7F [auth Z]286Homo sapiensMutation(s): 0 
Gene Names: PSMD7, MOV34L
Find proteins for P51665 (Homo sapiens)
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GTEx:  ENSG00000103035
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13G [auth a]373Homo sapiensMutation(s): 0 
Gene Names: PSMD13
Find proteins for Q9UNM6 (Homo sapiens)
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GTEx:  ENSG00000185627
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4H [auth b]191Homo sapiensMutation(s): 0 
Gene Names: PSMD4, MCB1
Find proteins for P55036 (Homo sapiens)
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GTEx:  ENSG00000159352
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14I [auth c]287Homo sapiensMutation(s): 0 
Gene Names: PSMD14, POH1
EC: 3.4.19
Find proteins for O00487 (Homo sapiens)
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GTEx:  ENSG00000115233
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Entity ID: 10
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26S proteasome non-ATPase regulatory subunit 8J [auth d]257Homo sapiensMutation(s): 0 
Gene Names: PSMD8
Find proteins for P48556 (Homo sapiens)
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GTEx:  ENSG00000099341
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1K [auth e]70Homo sapiensMutation(s): 0 
Gene Names: SEM1, C7orf76, DSS1, SHFDG1, SHFM1
Find proteins for P60896 (Homo sapiens)
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GTEx:  ENSG00000127922
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6L [auth G], Z [auth g]240Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
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GTEx:  ENSG00000100902
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2M [auth H], AA [auth h]232Homo sapiensMutation(s): 0 
Gene Names: PSMA2, HC3, PSC3
EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens)
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GTEx:  ENSG00000106588
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4N [auth I], BA [auth i]250Homo 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: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7O [auth J], CA [auth j]243Homo sapiensMutation(s): 0 
Gene Names: PSMA7, HSPC
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
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GTEx:  ENSG00000101182
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5P [auth K], DA [auth k]234Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
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GTEx:  ENSG00000143106
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1Q [auth L], EA [auth l]238Homo sapiensMutation(s): 0 
Gene Names: PSMA1, HC2, NU, PROS30, PSC2
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
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GTEx:  ENSG00000129084
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3R [auth M], FA [auth m]245Homo 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: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6S [auth N], GA [auth n]191Homo sapiensMutation(s): 0 
Gene Names: PSMB6, LMPY, Y
EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens)
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GTEx:  ENSG00000142507
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Entity ID: 20
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Proteasome subunit beta type-7T [auth O], HA [auth o]220Homo sapiensMutation(s): 0 
Gene Names: PSMB7, Z
EC: 3.4.25.1
Find proteins for Q99436 (Homo sapiens)
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GTEx:  ENSG00000136930
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3U [auth P], IA [auth p]204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
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GTEx:  ENSG00000277791
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2V [auth Q], JA [auth q]199Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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GTEx:  ENSG00000126067
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5W [auth R], KA [auth r]201Homo sapiensMutation(s): 0 
Gene Names: PSMB5, LMPX, MB1, X
EC: 3.4.25.1
Find proteins for P28074 (Homo sapiens)
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GTEx:  ENSG00000100804
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1X [auth S], LA [auth s]213Homo sapiensMutation(s): 0 
Gene Names: PSMB1, PSC5
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
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GTEx:  ENSG00000008018
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4Y [auth T], MA [auth t]215Homo sapiensMutation(s): 0 
Gene Names: PSMB4, PROS26
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
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GTEx:  ENSG00000159377
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7NA [auth A]399Homo sapiensMutation(s): 0 
Gene Names: PSMC2, MSS1
Find proteins for P35998 (Homo sapiens)
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GTEx:  ENSG00000161057
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Entity ID: 27
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26S proteasome regulatory subunit 4OA [auth B]389Homo sapiensMutation(s): 0 
Gene Names: PSMC1
Find proteins for P62191 (Homo sapiens)
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GTEx:  ENSG00000100764
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Entity ID: 28
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26S proteasome regulatory subunit 8PA [auth C]392Homo sapiensMutation(s): 0 
Gene Names: PSMC5, SUG1
Find proteins for P62195 (Homo sapiens)
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GTEx:  ENSG00000087191
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Entity ID: 29
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26S proteasome regulatory subunit 6BQA [auth D]380Homo sapiensMutation(s): 0 
Gene Names: PSMC4, MIP224, TBP7
Find proteins for P43686 (Homo sapiens)
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GTEx:  ENSG00000013275
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 10BRA [auth E]375Homo sapiensMutation(s): 0 
Gene Names: PSMC6, SUG2
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Entity ID: 31
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26S proteasome regulatory subunit 6ASA [auth F]396Homo sapiensMutation(s): 0 
Gene Names: PSMC3, TBP1
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GTEx:  ENSG00000165916
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Entity ID: 32
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26S proteasome non-ATPase regulatory subunit 2TA [auth f]908Homo sapiensMutation(s): 0 
Gene Names: PSMD2, TRAP2
Find proteins for Q13200 (Homo sapiens)
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GTEx:  ENSG00000175166
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS
Download Ideal Coordinates CCD File 
 VA [auth A], WA [auth B], XA [auth D], YA [auth F]PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
 UA [auth c]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1 ZIA BC011490
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCCR FLEX program
National Science Foundation (NSF, United States)United States1531991

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references
  • Version 1.2: 2020-11-18
    Changes: Database references