5LXY

Structure of the minimal RBM7 - ZCCHC8 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.262 

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

Structure of the RBM7-ZCCHC8 core of the NEXT complex reveals connections to splicing factors.

Falk, S.Finogenova, K.Melko, M.Benda, C.Lykke-Andersen, S.Jensen, T.H.Conti, E.

(2016) Nat Commun 7: 13573-13573

  • DOI: https://doi.org/10.1038/ncomms13573
  • Primary Citation of Related Structures:  
    5LXR, 5LXY

  • PubMed Abstract: 

    The eukaryotic RNA exosome participates extensively in RNA processing and degradation. In human cells, three accessory factors (RBM7, ZCCHC8 and hMTR4) interact to form the nuclear exosome targeting (NEXT) complex, which directs a subset of non-coding RNAs for exosomal degradation. Here we elucidate how RBM7 is incorporated in the NEXT complex. We identify a proline-rich segment of ZCCHC8 as the interaction site for the RNA-recognition motif (RRM) of RBM7 and present the crystal structure of the corresponding complex at 2.0 Å resolution. On the basis of the structure, we identify a proline-rich segment within the splicing factor SAP145 with strong similarity to ZCCHC8. We show that this segment of SAP145 not only binds the RRM region of another splicing factor SAP49 but also the RRM of RBM7. These dual interactions of RBM7 with the exosome and the spliceosome suggest a model whereby NEXT might recruit the exosome to degrade intronic RNAs.


  • Organizational Affiliation

    Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 7
A,
C [auth B],
E,
G,
I,
K,
M
90Homo 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger CCHC domain-containing protein 845Homo sapiensMutation(s): 0 
Gene Names: ZCCHC8
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NZY4 (Homo sapiens)
Explore Q6NZY4 
Go to UniProtKB:  Q6NZY4
PHAROS:  Q6NZY4
GTEx:  ENSG00000033030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NZY4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download Ideal Coordinates CCD File 
O [auth D]
P [auth C]
Q [auth C]
R [auth F]
S [auth G]
O [auth D],
P [auth C],
Q [auth C],
R [auth F],
S [auth G],
T [auth H],
U [auth J],
V [auth L],
W [auth N]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.262 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.771α = 90
b = 66.575β = 126.57
c = 111.912γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
xia2data reduction
Aimlessdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description