6WJD

SA-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: 2020-04-13 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: 4.80 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]953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
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GTEx:  ENSG00000173692 
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Entity ID: 2
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26S proteasome non-ATPase regulatory subunit 3B [auth V]534Homo sapiensMutation(s): 0 
Gene Names: PSMD3
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GTEx:  ENSG00000108344 
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Entity ID: 3
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26S proteasome non-ATPase regulatory subunit 12C [auth W]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 X]422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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GTEx:  ENSG00000108671 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6E [auth Y]389Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7F [auth Z]324Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
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GTEx:  ENSG00000103035 
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Entity ID: 7
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26S proteasome non-ATPase regulatory subunit 13G [auth a]376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
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Entity ID: 8
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26S proteasome non-ATPase regulatory subunit 4H [auth b]377Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14I [auth c]309Homo sapiensMutation(s): 0 
Gene Names: PSMD14POH1
EC: 3.4.19
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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]349Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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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: SEM1C7orf76DSS1SHFDG1SHFM1
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26S proteasome non-ATPase regulatory subunit 2L [auth f]908Homo sapiensMutation(s): 0 
Gene Names: PSMD2TRAP2
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GTEx:  ENSG00000175166 
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Entity ID: 13
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26S proteasome regulatory subunit 7M [auth A]433Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
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GTEx:  ENSG00000161057 
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26S proteasome regulatory subunit 4N [auth B]440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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GTEx:  ENSG00000100764 
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Entity ID: 15
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26S proteasome regulatory subunit 8O [auth C]398Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
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GTEx:  ENSG00000087191 
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Entity ID: 16
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26S proteasome regulatory subunit 6BP [auth D]418Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
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GTEx:  ENSG00000013275 
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Entity ID: 17
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26S proteasome regulatory subunit 10BQ [auth E]403Homo sapiensMutation(s): 0 
Gene Names: PSMC6
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GTEx:  ENSG00000100519 
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Entity ID: 18
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26S proteasome regulatory subunit 6AR [auth F]439Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
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GTEx:  ENSG00000165916 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinS [auth u]76Homo sapiensMutation(s): 0 
Gene Names: UBC
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6T [auth G],
HA [auth g]
245Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2U [auth H],
IA [auth h]
233Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4V [auth I],
JA [auth i]
260Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
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GTEx:  ENSG00000041357 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7W [auth J],
KA [auth j]
247Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
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GTEx:  ENSG00000101182 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5X [auth K],
LA [auth k]
240Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1Y [auth L],
MA [auth l]
268Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3Z [auth M],
NA [auth m]
254Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6AA [auth N],
OA [auth n]
238Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7BA [auth O],
PA [auth o]
276Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3CA [auth P],
QA [auth p]
204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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GTEx:  ENSG00000277791 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2DA [auth Q],
RA [auth q]
201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5EA [auth R],
SA [auth r]
262Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1FA [auth S],
TA [auth s]
240Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4GA [auth T],
UA [auth t]
263Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

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BB [auth D],
DB [auth E],
WA [auth A],
YA [auth B]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

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AB [auth C],
FB [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
VA [auth c]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
CB [auth D],
EB [auth E],
GB [auth F],
XA [auth A],
ZA [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 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