4WJV

Crystal structure of Rsa4 in complex with the Nsa2 binding peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation.

Baler, J.Paternoga, H.Holdermann, I.Thoms, M.Granneman, S.Barrio-Garcia, C.Nyarko, A.Stier, G.Clark, S.A.Schraivogel, D.Kallas, M.Beckmann, R.Tollervey, D.Barbar, E.Sinning, I.Hurt, E.

(2014) J Cell Biol 207: 481-498

  • DOI: 10.1083/jcb.201408111
  • Primary Citation of Related Structures:  
    4WJS, 4WJU, 4WJV, 2MVF

  • PubMed Abstract: 
  • Eukaryotic ribosome biogenesis involves ∼200 assembly factors, but how these contribute to ribosome maturation is poorly understood. Here, we identify a network of factors on the nascent 60S subunit that actively remodels preribosome structure. At its hub is Rsa4, a direct substrate of the force-generating ATPase Rea1 ...

    Eukaryotic ribosome biogenesis involves ∼200 assembly factors, but how these contribute to ribosome maturation is poorly understood. Here, we identify a network of factors on the nascent 60S subunit that actively remodels preribosome structure. At its hub is Rsa4, a direct substrate of the force-generating ATPase Rea1. We show that Rsa4 is connected to the central protuberance by binding to Rpl5 and to ribosomal RNA (rRNA) helix 89 of the nascent peptidyl transferase center (PTC) through Nsa2. Importantly, Nsa2 binds to helix 89 before relocation of helix 89 to the PTC. Structure-based mutations of these factors reveal the functional importance of their interactions for ribosome assembly. Thus, Rsa4 is held tightly in the preribosome and can serve as a "distribution box," transmitting remodeling energy from Rea1 into the developing ribosome. We suggest that a relay-like factor network coupled to a mechano-enzyme is strategically positioned to relocate rRNA elements during ribosome maturation.


    Organizational Affiliation

    Biochemistry Center of Heidelberg University, INF328, D-69120 Heidelberg, Germany ed.hurt@bzh.uni-heidelberg.de irmi.sinning@bzh.uni-heidelberg.de barbare@science.oregonstate.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome assembly protein 4A, B, C, D381Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RSA4YCR072CYCR72C
UniProt
Find proteins for P25382 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25382 
Go to UniProtKB:  P25382
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic proteinE, F, G, H381Escherichia coli K-12Mutation(s): 7 
Gene Names: malEb4034JW3994
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AEX9
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2I, J, K, L22Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSA2YER126CSYGP-ORF47
UniProt
Find proteins for P40078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40078 
Go to UniProtKB:  P40078
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseM, N, O, P2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
M, N, O, Palpha-maltoseOligosaccharide /  Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 198.578α = 90
b = 96.493β = 115.45
c = 196.445γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 1.2: 2014-12-10
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary