4WYK

Structure of the LRR and NTF2-like domains of NXF1 complexed with NXT1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The principal mRNA nuclear export factor NXF1:NXT1 forms a symmetric binding platform that facilitates export of retroviral CTE-RNA.

Aibara, S.Katahira, J.Valkov, E.Stewart, M.

(2015) Nucleic Acids Res 43: 1883-1893

  • DOI: https://doi.org/10.1093/nar/gkv032
  • Primary Citation of Related Structures:  
    4WYK

  • PubMed Abstract: 

    The NXF1:NXT1 complex (also known as TAP:p15) is a general mRNA nuclear export factor that is conserved from yeast to humans. NXF1 is a modular protein constructed from four domains (RRM, LRR, NTF2-like and UBA domains). It is currently unclear how NXF1:NXT1 binds transcripts and whether there is higher organization of the NXF1 domains. We report here the 3.4 Å resolution crystal structure of the first three domains of human NXF1 together with NXT1 that has two copies of the complex in the asymmetric unit arranged to form an intimate domain-swapped dimer. In this dimer, the linkers between the NXF1 LRR and NTF2-like domains interact with NXT1, generating a 2-fold symmetric platform in which the RNA-binding RRM, LRR and NTF2-like domains are arranged on one face. In addition to bulk transcripts, NXF1:NXT1 also facilitates the export of unspliced retroviral genomic RNA from simple type-D retroviruses such as SRV-1 that contain a constitutive transport element (CTE), a cis-acting 2-fold symmetric RNA stem-loop motif. Complementary structural, biochemical and cellular techniques indicated that the formation of a symmetric RNA binding platform generated by dimerization of NXF1:NXT1 facilitates the recognition of CTE-RNA and promotes its nuclear export.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear RNA export factor 1
A, C
461Homo sapiensMutation(s): 0 
Gene Names: NXF1TAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBU9 (Homo sapiens)
Explore Q9UBU9 
Go to UniProtKB:  Q9UBU9
PHAROS:  Q9UBU9
GTEx:  ENSG00000162231 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBU9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NTF2-related export protein 1
B, D
139Homo sapiensMutation(s): 0 
Gene Names: NXT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKK6 (Homo sapiens)
Explore Q9UKK6 
Go to UniProtKB:  Q9UKK6
PHAROS:  Q9UKK6
GTEx:  ENSG00000132661 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKK6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.046α = 108.69
b = 83.972β = 99.76
c = 108.233γ = 97.51
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomU105178939

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Database references
  • Version 1.2: 2015-02-25
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence