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: https://doi.org/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. 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

    John M. Cowley Center for High Resolution Electron Microscopy, Arizona State University, Tempe, AZ 85287, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1A [auth U]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 V]534Homo 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 W]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 X]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 Y]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 Z]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 a]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 b]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 c]309Homo 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 d]349Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099341 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1K [auth e]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 f]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175166 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7M [auth A]433Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161057 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4N [auth B]440Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100764 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8O [auth C]398Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087191 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6BP [auth D]418Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000013275 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 10BQ [auth E]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100519 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6AR [auth F]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165916 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinS [auth u]76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150991 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6HA [auth g],
T [auth G]
245Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2IA [auth h],
U [auth H]
233Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4JA [auth i],
V [auth I]
260Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000041357 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7KA [auth j],
W [auth J]
247Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000101182 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5LA [auth k],
X [auth K]
240Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1MA [auth l],
Y [auth L]
268Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3NA [auth m],
Z [auth M]
254Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6AA [auth N],
OA [auth n]
238Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7BA [auth O],
PA [auth o]
276Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3CA [auth P],
QA [auth p]
204Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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PHAROS:  P49720
GTEx:  ENSG00000277791 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2DA [auth Q],
RA [auth q]
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5EA [auth R],
SA [auth r]
262Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1FA [auth S],
TA [auth s]
240Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4GA [auth T],
UA [auth t]
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
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
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AB [auth C],
FB [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
VA [auth c]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.8
MODEL REFINEMENTPHENIX1.17.1-3660

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