6JWI

Yeast Npl4 in complex with Lys48-linked diubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4.

Sato, Y.Tsuchiya, H.Yamagata, A.Okatsu, K.Tanaka, K.Saeki, Y.Fukai, S.

(2019) Nat Commun 10: 5708-5708

  • DOI: https://doi.org/10.1038/s41467-019-13697-y
  • Primary Citation of Related Structures:  
    6JWH, 6JWI, 6JWJ

  • PubMed Abstract: 

    Npl4 is likely to be the most upstream factor recognizing Lys48-linked polyubiquitylated substrates in the proteasomal degradation pathway in yeast. Along with Ufd1, Npl4 forms a heterodimer (UN), and functions as a cofactor for the Cdc48 ATPase. Here, we report the crystal structures of yeast Npl4 in complex with Lys48-linked diubiquitin and with the Npl4-binding motif of Ufd1. The distal and proximal ubiquitin moieties of Lys48-linked diubiquitin primarily interact with the C-terminal helix and N-terminal loop of the Npl4 C-terminal domain (CTD), respectively. Mutational analysis suggests that the CTD contributes to linkage selectivity and initial binding of ubiquitin chains. Ufd1 occupies a hydrophobic groove of the Mpr1/Pad1 N-terminal (MPN) domain of Npl4, which corresponds to the catalytic groove of the MPN domain of JAB1/MPN/Mov34 metalloenzyme (JAMM)-family deubiquitylating enzyme. This study provides important structural insights into the polyubiquitin chain recognition by the Cdc48-UN complex and its assembly.


  • Organizational Affiliation

    Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UbiqutinA [auth I],
D [auth G]
76Mus musculusMutation(s): 0 
Gene Names: UbcEG216818
UniProt
Find proteins for P62984 (Mus musculus)
Explore P62984 
Go to UniProtKB:  P62984
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62984
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear protein localization protein 4B [auth A],
C [auth E]
473Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NPL4HRD4YBR170CYBR1231
UniProt
Find proteins for P33755 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33755 
Go to UniProtKB:  P33755
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33755
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCN
Query on BCN

Download Ideal Coordinates CCD File 
BA [auth E]
CA [auth E]
DA [auth E]
EA [auth E]
U [auth A]
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth E],
S [auth A],
T [auth A],
Z [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth I],
D [auth G]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.351α = 90
b = 103.103β = 100.401
c = 99.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16H04750
Japan Society for the Promotion of ScienceJapan15H01175
Japan Society for the Promotion of ScienceJapan18H05501

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary