8DAU

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two folded ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (uA)

  • Classification: MOTOR PROTEIN
  • Organism(s): Saccharomyces cerevisiae
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-06-14 Released: 2022-11-30 
  • Deposition Author(s): Lee, H.G., Lima, C.D.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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

SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex.

Lee, H.G.Lemmon, A.A.Lima, C.D.

(2023) Proc Natl Acad Sci U S A 120: e2213703120-e2213703120

  • DOI: https://doi.org/10.1073/pnas.2213703120
  • Primary Citation of Related Structures:  
    8DAR, 8DAS, 8DAT, 8DAU, 8DAV, 8DAW

  • PubMed Abstract: 

    The Ufd1/Npl4/Cdc48 complex is a universal protein segregase that plays key roles in eukaryotic cellular processes. Its functions orchestrating the clearance or removal of polyubiquitylated targets are established; however, prior studies suggest that the complex also targets substrates modified by the ubiquitin-like protein SUMO. Here, we show that interactions between Ufd1 and SUMO enhance unfolding of substrates modified by SUMO-polyubiquitin hybrid chains by the budding yeast Ufd1/Npl4/Cdc48 complex compared to substrates modified by polyubiquitin chains, a difference that is accentuated when the complex has a choice between these substrates. Incubating Ufd1/Npl4/Cdc48 with a substrate modified by a SUMO-polyubiquitin hybrid chain produced a series of single-particle cryo-EM structures that reveal features of interactions between Ufd1/Npl4/Cdc48 and ubiquitin prior to and during unfolding of ubiquitin. These results are consistent with cellular functions for SUMO and ubiquitin modifications and support a physical model wherein Ufd1/Npl4/Cdc48, SUMO, and ubiquitin conjugation pathways converge to promote clearance of proteins modified with SUMO and polyubiquitin.


  • Organizational Affiliation

    Biochemistry, Structural Biology, Cell Biology, Developmental Biology and Molecular Biology (BCMB) Allied Program, Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10065.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 48
A, B, C, D, E
A, B, C, D, E, F
838Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC48YDL126C
EC: 3.6.4.6
UniProt
Find proteins for P25694 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25694 
Go to UniProtKB:  P25694
Entity Groups  
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UniProt GroupP25694
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear protein localization protein 4583Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NPL4HRD4YBR170CYBR1231
UniProt
Find proteins for P33755 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33755 
Go to UniProtKB:  P33755
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UniProt GroupP33755
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin fusion degradation protein 1363Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: UFD1PIP3YGR048W
UniProt
Find proteins for P53044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53044 
Go to UniProtKB:  P53044
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UniProt GroupP53044
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin
I, J, K
76Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: UBI4SCD2YLL039C
UniProt
Find proteins for P0CG63 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CG63 
Go to UniProtKB:  P0CG63
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UniProt GroupP0CG63
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
L [auth A],
N [auth B],
P [auth C],
R [auth D],
V [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
M [auth A]
O [auth B]
Q [auth C]
S [auth D]
T [auth E]
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
T [auth E],
U [auth E],
W [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
X [auth G],
Y [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118080
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary