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 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1038/s41467-019-13697-y
  • Primary Citation of Related Structures:  

  • 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. Her ...

    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

    Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan. fukai@iam.u-tokyo.ac.jp.,RIKEN Center for Biosystems Dynamics Research, Kanagawa, 230-0045, Japan.,Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan. saeki-ys@igakuken.or.jp.,Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, 680-8582, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan.,Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan. fukai@iam.u-tokyo.ac.jp.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan. fukai@iam.u-tokyo.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiqutin
I, G
76Mus musculusMutation(s): 0 
Gene Names: Ubc (EG216818)
Find proteins for A5JUZ1 (Mus musculus)
Go to UniProtKB:  A5JUZ1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear protein localization protein 4
A, E
473Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NPL4 (HRD4)
Find proteins for P33755 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33755
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRE
Query on TRE

Download SDF File 
Download CCD File 
A, E
TREHALOSE
ALPHA-D-GLUCOPYRANOSYL-ALPHA-D-GLUCOPYRANOSIDE
C12 H22 O11
HDTRYLNUVZCQOY-LIZSDCNHSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BCN
Query on BCN

Download SDF File 
Download CCD File 
A, E
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
G, I
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 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.351α = 90.00
b = 103.103β = 100.40
c = 99.620γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-04-20 
  • Released Date: 2019-12-25 
  • Deposition Author(s): Sato, Y., Fukai, S.

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 

  • Version 1.0: 2019-12-25
    Type: Initial release