8J4A

Crystal structure of OY phytoplasma SAP05 in complex with AtRPN10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis of SAP05-mediated ubiquitin-independent proteasomal degradation of transcription factors.

Yan, X.Yuan, X.Lv, J.Zhang, B.Huang, Y.Li, Q.Ma, J.Li, Y.Wang, X.Li, Y.Yu, Y.Liu, Q.Liu, T.Mi, W.Dong, C.

(2024) Nat Commun 15: 1170-1170

  • DOI: https://doi.org/10.1038/s41467-024-45521-7
  • Primary Citation of Related Structures:  
    8J48, 8J49, 8J4A, 8J4B

  • PubMed Abstract: 

    SAP05, a secreted effector by the obligate parasitic bacteria phytoplasma, bridges host SPL and GATA transcription factors (TFs) to the 26 S proteasome subunit RPN10 for ubiquitination-independent degradation. Here, we report the crystal structures of SAP05 in complex with SPL5, GATA18 and RPN10, which provide detailed insights into the protein-protein interactions involving SAP05. SAP05 employs two opposing lobes with an acidic path and a hydrophobic path to contact TFs and RPN10, respectively. Our crystal structures, in conjunction with mutagenesis and degradation assays, reveal that SAP05 targets plant GATAs but not animal GATAs dependent on their direct salt-bridged electrostatic interactions. Additionally, SAP05 hijacks plant RPN10 but not animal RPN10 due to structural steric hindrance and the key hydrophobic interactions. This study provides valuable molecular-level information into the modulation of host proteins to prevent insect-borne diseases.


  • Organizational Affiliation

    The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sequence-variable mosaic (SVM) signal sequence domain-containing proteinA,
B [auth C]
104Onion yellows phytoplasma OY-MMutation(s): 0 
Gene Names: PAM_518
UniProt
Find proteins for Q6YQ57 (Onion yellows phytoplasma (strain OY-M))
Explore Q6YQ57 
Go to UniProtKB:  Q6YQ57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6YQ57
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4 homologC [auth D],
D [auth B]
194Arabidopsis thalianaMutation(s): 0 
Gene Names: RPN10MBP1MCB1At4g38630F20M13.190T9A14.7
UniProt
Find proteins for P55034 (Arabidopsis thaliana)
Explore P55034 
Go to UniProtKB:  P55034
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55034
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.045α = 90
b = 40.586β = 93.013
c = 130.329γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31900865
National Natural Science Foundation of China (NSFC)China32271265
National Natural Science Foundation of China (NSFC)China32071193
National Natural Science Foundation of China (NSFC)China81874039

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Structure summary
  • Version 1.2: 2024-05-08
    Changes: Database references