PDBsum entry 5cxc

Protein binding

PDB id: 5cxc

Contents

Protein chains

452 a.a.

348 a.a.

Metals

_CL ×2

PDB id:

5cxc

Name:

Protein binding

Title:

Structure of ytm1 bound to thE C-terminal domain of erb1 in p 65 2 2 space group

Structure:

Ribosome biogenesis protein ytm1. Chain: a. Fragment: unp residues 433-801. Engineered: yes. Ribosome biogenesis protein erb1. Chain: b. Synonym: eukaryotic ribosome biogenesis protein 1. Engineered: yes

Source:

Chaetomium thermophilum. Organism_taxid: 209285. Gene: ytm1, ctht_0061460. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9. Gene: erb1, ctht_0057570. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

3.10Å R-factor: 0.196 R-free: 0.239

Authors:

M.Wegrecki,J.Bravo

Key ref:

M.Wegrecki et al. (2015). The structure of Erb1-Ytm1 complex reveals the functional importance of a high-affinity binding between two β-propellers during the assembly of large ribosomal subunits in eukaryotes. Nucleic Acids Res, 43, 11017-11030. PubMed id: 26476442 DOI: 10.1093/nar/gkv1043

Date:

28-Jul-15 Release date: 28-Oct-15

Protein chain

G0SFB5  (YTM1_CHATD) -  Ribosome biogenesis protein YTM1 from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

Seq: 495 a.a.

Struc: 452 a.a.

Protein chain

G0SCK6  (ERB1_CHATD) -  Ribosome biogenesis protein ERB1 from Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

Seq: 801 a.a.

Struc: 348 a.a.

DOI no: 10.1093/nar/gkv1043

Nucleic Acids Res 43:11017-11030 (2015)

PubMed id: 26476442

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

M.Wegrecki, O.Rodríguez-Galán, J.de la Cruz, J.Bravo.

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.