8GXL

HUMAN SUGP1 433-577

  • Classification: RNA BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-09-20 Released: 2022-12-14 
  • Deposition Author(s): Xu, K., Tong, L.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

DHX15 is involved in SUGP1-mediated RNA missplicing by mutant SF3B1 in cancer.

Zhang, J.Huang, J.Xu, K.Xing, P.Huang, Y.Liu, Z.Tong, L.Manley, J.L.

(2022) Proc Natl Acad Sci U S A 119: e2216712119-e2216712119

  • DOI: https://doi.org/10.1073/pnas.2216712119
  • Primary Citation of Related Structures:  
    8EJM, 8GXL, 8GXM

  • PubMed Abstract: 

    SF3B1 is the most frequently mutated spliceosomal gene in cancer. Several hotspot mutations are known to disrupt the interaction of SF3B1 with another splicing factor, SUGP1, resulting in the RNA missplicing that characterizes mutant SF3B1 cancers. Properties of SUGP1, especially the presence of a G-patch motif, a structure known to function by activating DEAH-box RNA helicases, suggest the requirement of such an enzyme in SUGP1 function in splicing. However, the identity of this putative helicase has remained an important unanswered question. Here, using a variety of protein-protein interaction assays, we identify DHX15 as the critical helicase. We further show that depletion of DHX15 or expression of any of several DHX15 mutants, including one implicated in acute myeloid leukemia, partially recapitulates the splicing defects of mutant SF3B1. Moreover, a DHX15-SUGP1 G-patch fusion protein is able to incorporate into the spliceosome to rescue the splicing defects of mutant SF3B1. We also present the crystal structure of the human DHX15-SUGP1 G-patch complex, which reveals the molecular basis of their direct interaction. Our data thus demonstrate that DHX15 is the RNA helicase that functions with SUGP1 and additionally provide important insight into how mutant SF3B1 disrupts splicing in cancer.


  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SURP and G-patch domain-containing protein 1
A, B
145Homo sapiensMutation(s): 0 
Gene Names: SUGP1SF4
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IWZ8 (Homo sapiens)
Explore Q8IWZ8 
Go to UniProtKB:  Q8IWZ8
PHAROS:  Q8IWZ8
GTEx:  ENSG00000105705 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IWZ8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.204 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.657α = 90
b = 59.657β = 90
c = 178.404γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
Cootmodel building
PHENIXphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118093

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection