5CXB

Structure of Ytm1 bound to the C-terminal domain of Erb1 in P21 21 2 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of Erb1-Ytm1 complex reveals the functional importance of a high-affinity binding between two beta-propellers during the assembly of large ribosomal subunits in eukaryotes.

Wegrecki, M.Rodriguez-Galan, O.de la Cruz, J.Bravo, J.

(2015) Nucleic Acids Res 43: 11017-11030

  • DOI: https://doi.org/10.1093/nar/gkv1043
  • Primary Citation of Related Structures:  
    5CXB, 5CXC, 5CYK

  • PubMed Abstract: 

    Ribosome biogenesis is one of the most essential pathways in eukaryotes although it is still not fully characterized. Given the importance of this process in proliferating cells, it is obvious that understanding the macromolecular details of the interactions that take place between the assembly factors, ribosomal proteins and nascent pre-rRNAs is essentially required for the development of new non-genotoxic treatments for cancer. Herein, we have studied the association between the WD40-repeat domains of Erb1 and Ytm1 proteins. These are essential factors for the biogenesis of 60S ribosomal subunits in eukaryotes that form a heterotrimeric complex together with the also essential Nop7 protein. We provide the crystal structure of a dimer formed by the C-terminal part of Erb1 and Ytm1 from Chaetomium thermophilum at 2.1 Å resolution. Using a multidisciplinary approach we show that the β-propeller domains of these proteins interact in a novel manner that leads to a high-affinity binding. We prove that a point mutation within the interface of the complex impairs the interaction between the two proteins and negatively affects growth and ribosome production in yeast. Our study suggests insights into the association of the Erb1-Ytm1 dimer with pre-ribosomal particles.


  • Organizational Affiliation

    Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, c/ Jaime Roig 11, 46010 Valencia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein YTM1514Thermochaetoides thermophilaMutation(s): 0 
Gene Names: YTM1CTHT_0061460
UniProt
Find proteins for G0SFB5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SFB5 
Go to UniProtKB:  G0SFB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SFB5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ERB1369Thermochaetoides thermophilaMutation(s): 0 
Gene Names: ERB1CTHT_0057570
UniProt
Find proteins for G0SCK6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SCK6 
Go to UniProtKB:  G0SCK6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SCK6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.443α = 90
b = 108.149β = 90
c = 108.618γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2015-12-23
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description