5IQQ

Crystal structure of the human RBM7 RRM domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

Starting Models: experimental
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This is version 1.2 of the entry. See complete history


Literature

RRM domain of human RBM7: purification, crystallization and structure determination.

Sofos, N.Winkler, M.B.Brodersen, D.E.

(2016) Acta Crystallogr F Struct Biol Commun 72: 397-402

  • DOI: https://doi.org/10.1107/S2053230X16006129
  • Primary Citation of Related Structures:  
    5IQQ

  • PubMed Abstract: 

    RNA decay is an important process that is essential for controlling the abundance, quality and maturation of transcripts. In eukaryotes, RNA decay in the 3'-5' direction is carried out by the exosome, an RNA-degradation machine that is conserved from yeast to humans. A range of cofactors stimulate the enzymatic activity of the exosome and serve as adapters for the many RNA substrates. In human cells, the exosome associates with the heterotrimeric nuclear exosome targeting (NEXT) complex consisting of the DExH-box helicase hMTR4, the zinc-finger protein hZCCHC8 and the RRM-type protein hRBM7. Here, the 2.5 Å resolution crystal structure of the RRM domain of human RBM7 is reported. Molecular replacement using a previously determined solution structure of RBM7 was unsuccessful. Instead, RBM8 and CBP20 RRM-domain crystal structures were used to successfully determine the RBM7 structure by molecular replacement. The structure reveals a ring-shaped pentameric assembly, which is most likely a consequence of crystal packing.


  • Organizational Affiliation

    Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 7
A, B, C, D, E
91Homo sapiensMutation(s): 0 
Gene Names: RBM7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y580 (Homo sapiens)
Explore Q9Y580 
Go to UniProtKB:  Q9Y580
PHAROS:  Q9Y580
GTEx:  ENSG00000076053 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y580
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.707α = 90
b = 83.21β = 119.63
c = 60.826γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish National Research Foundation and Novo Nordisk FoundationDenmarkDNRF58

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description