7EA2

crystal structure of NAP1 FIR in complex with RB1CC1 Claw domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and biochemical advances on the recruitment of the autophagy-initiating ULK and TBK1 complexes by autophagy receptor NDP52.

Fu, T.Zhang, M.Zhou, Z.Wu, P.Peng, C.Wang, Y.Gong, X.Li, Y.Wang, Y.Xu, X.Li, M.Shen, L.Pan, L.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abi6582
  • Primary Citation of Related Structures:  
    7EA2, 7EA7, 7EAA

  • PubMed Abstract: 

    The recruitment of Unc-51-like kinase and TANK-binding kinase 1 complexes is essential for Nuclear dot protein 52-mediated selective autophagy and relies on the specific association of NDP52, RB1-inducible coiled-coil protein 1, and Nak-associated protein 1 (5-azacytidine-induced protein 2, AZI2). However, the underlying molecular mechanism remains elusive. Here, we find that except for the NDP52 SKIP carboxyl homology (SKICH)/RB1CC1 coiled-coil interaction, the LC3-interacting region of NDP52 can directly interact with the RB1CC1 Claw domain, as that of NAP1 FIP200-binding region (FIR). The determined crystal structures of NDP52 SKICH/RB1CC1 complex, NAP1 FIR/RB1CC1 complex, and the related NAP1 FIR/Gamma-aminobutyric acid receptor-associated protein complex not only elucidate the molecular bases underpinning the interactions of RB1CC1 with NDP52 and NAP1 but also reveal that RB1CC1 Claw and Autophagy-related protein 8 family proteins are competitive in binding to NAP1 and NDP52. Overall, our findings provide mechanistic insights into the interactions of NDP52, NAP1 with RB1CC1 and ATG8 family proteins.


  • Organizational Affiliation

    State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-azacytidine-induced protein 2,RB1-inducible coiled-coil protein 1A [auth B],
B [auth A]
124Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDY2 (Homo sapiens)
Explore Q8TDY2 
Go to UniProtKB:  Q8TDY2
PHAROS:  Q8TDY2
GTEx:  ENSG00000023287 
Find proteins for Q9H6S1 (Homo sapiens)
Explore Q9H6S1 
Go to UniProtKB:  Q9H6S1
PHAROS:  Q9H6S1
GTEx:  ENSG00000163512 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9H6S1Q8TDY2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.62α = 90
b = 67.62β = 90
c = 247.37γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2021-12-22 
  • Deposition Author(s): Fu, T., Pan, L.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21672253
National Natural Science Foundation of China (NSFC)China21822705
National Natural Science Foundation of China (NSFC)China21621002

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description