7WWP

Crystal structure of human Npl4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the interaction between human Npl4 and Npl4-binding motif of human Ufd1.

Nguyen, T.Q.My Le, L.T.Kim, D.H.Ko, K.S.Lee, H.T.Kim Nguyen, Y.T.Kim, H.S.Han, B.W.Kang, W.Yang, J.K.

(2022) Structure 30: 1530-1537.e3

  • DOI: https://doi.org/10.1016/j.str.2022.08.005
  • Primary Citation of Related Structures:  
    7WWP, 7WWQ

  • PubMed Abstract: 

    The heterodimer of human ubiquitin fusion degradation 1 (hUfd1) and human nuclear protein localization 4 (hNpl4) is a major cofactor of human p97 adenosine triphosphatase (ATPase). The p97-Ufd1-Npl4 complex translocates the ubiquitin-conjugated proteins from the endoplasmic reticulum membrane to the cytoplasm. Ubiquitinated proteins are then degraded by the proteasome. The structures of Npl4 and Ufd1-Npl4 (UN) complex in Saccharomyces cerevisiae have been recently reported; however, the structures of hNpl4 and the human UN complex remain unknown. Here, we report the crystal structures of the human UN complex at a resolution of 2.7 Å and hNpl4 at a resolution of 3.0 Å. We also present atomic details and characterization of the human UN complex. Crystallographic studies and site-directed mutagenesis of the hUfd1 residues involved in the interaction with hNpl4 revealed the atomic details of the two proteins.


  • Organizational Affiliation

    Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear protein localization protein 4 homolog473Homo sapiensMutation(s): 0 
Gene Names: NPLOC4NPL4
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAT6 (Homo sapiens)
Explore Q8TAT6 
Go to UniProtKB:  Q8TAT6
PHAROS:  Q8TAT6
GTEx:  ENSG00000182446 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TAT6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.325α = 90
b = 136.325β = 90
c = 126.875γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2014R1A2A2A01006834
National Research Foundation (NRF, Korea)Korea, Republic Of2017R1D1A1B03035446
National Research Foundation (NRF, Korea)Korea, Republic Of2019R1F1A106326813
National Research Foundation (NRF, Korea)Korea, Republic Of2021R1A6A1A10044154

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2022-11-16
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description