5AFF

Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report



Literature

Symportin 1 Chaperones 5S Rnp Assembly During Ribosome Biogenesis by Occupying an Essential Rrna-Binding Site.

Calvino, F.R.Kharde, S.Ori, A.Hendricks, A.Wild, K.Kressler, D.Bange, G.Hurt, E.Beck, M.Sinning, I.

(2015) Nat Commun 6: 6510

  • DOI: 10.1038/ncomms7510
  • Primary Citation of Related Structures:  
    5AFF

  • PubMed Abstract: 
  • During 60S biogenesis, mature 5S RNP consisting of 5S RNA, RpL5 and RpL11, assembles into a pre-60S particle, where docking relies on RpL11 interacting with helix 84 (H84) of the 25S RNA. How 5S RNP is assembled for recruitment into the pre-60S is no ...

    During 60S biogenesis, mature 5S RNP consisting of 5S RNA, RpL5 and RpL11, assembles into a pre-60S particle, where docking relies on RpL11 interacting with helix 84 (H84) of the 25S RNA. How 5S RNP is assembled for recruitment into the pre-60S is not known. Here we report the crystal structure of a ternary symportin Syo1-RpL5-N-RpL11 complex and provide biochemical and structural insights into 5S RNP assembly. Syo1 guards the 25S RNA-binding surface on RpL11 and competes with H84 for binding. Pull-down experiments show that H84 releases RpL11 from the ternary complex, but not in the presence of 5S RNA. Crosslinking mass spectrometry visualizes structural rearrangements on incorporation of 5S RNA into the Syo1-RpL5-RpL11 complex supporting the formation of a pre-5S RNP. Our data underline the dual role of Syo1 in ribosomal protein transport and as an assembly platform for 5S RNP.


    Organizational Affiliation

    Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SYMPORTIN 1A654Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S5S6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0S5S6
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L5B48Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SEG2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0SEG2
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L11C173Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SHQ2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SHQ2 
Go to UniProtKB:  G0SHQ2
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.087α = 90
b = 105.959β = 90
c = 147.234γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release