4XD9 | pdb_00004xd9

Structure of Rpf2-Rrs1 complex involved in ribosome biogenesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.235 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4XD9

This is version 1.2 of the entry. See complete history

Literature

Structural and functional analysis of the Rpf2-Rrs1 complex in ribosome biogenesis.

Asano, N.Kato, K.Nakamura, A.Komoda, K.Tanaka, I.Yao, M.

(2015) Nucleic Acids Res 43: 4746-4757

  • DOI: https://doi.org/10.1093/nar/gkv305
  • Primary Citation Related Structures: 
    4XD9

  • PubMed Abstract: 

    Proteins Rpf2 and Rrs1 are required for 60S ribosomal subunit maturation. These proteins are necessary for the recruitment of three ribosomal components (5S ribosomal RNA [rRNA], RpL5 and RpL11) to the 90S ribosome precursor and subsequent 27SB pre-rRNA processing. Here we present the crystal structure of the Aspergillus nidulans (An) Rpf2-Rrs1 core complex. The core complex contains the tightly interlocked N-terminal domains of Rpf2 and Rrs1. The Rpf2 N-terminal domain includes a Brix domain characterized by similar N- and C-terminal architecture. The long α-helix of Rrs1 joins the C-terminal half of the Brix domain as if it were part of a single molecule. The conserved proline-rich linker connecting the N- and C-terminal domains of Rrs1 wrap around the side of Rpf2 and anchor the C-terminal domain of Rrs1 to a specific site on Rpf2. In addition, gel shift analysis revealed that the Rpf2-Rrs1 complex binds directly to 5S rRNA. Further analysis of Rpf2-Rrs1 mutants demonstrated that Saccharomyces cerevisiae Rpf2 R236 (corresponds to R238 of AnRpf2) plays a significant role in this binding. Based on these studies and previous reports, we have proposed a model for ribosomal component recruitment to the 90S ribosome precursor.


  • Organizational Affiliation
    • Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan.

Macromolecule Content 

  • Total Structure Weight: 122.82 kDa 
  • Atom Count: 5,165 
  • Modeled Residue Count: 646 
  • Deposited Residue Count: 1,088 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein, putative (AFU_orthologue AFUA_8G04790)
A, C
323Aspergillus nidulans FGSC A4Mutation(s): 0 
Gene Names: AN3745.2ANIA_03745
UniProt
Find proteins for C8VMF9 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore C8VMF9 
Go to UniProtKB:  C8VMF9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC8VMF9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein (Rrs1), putative (AFU_orthologue AFUA_7G04430)
B, D
221Aspergillus nidulans FGSC A4Mutation(s): 0 
Gene Names: ANIA_10200
UniProt
Find proteins for Q5B6T5 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore Q5B6T5 
Go to UniProtKB:  Q5B6T5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5B6T5
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.235 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.163α = 90
b = 123.594β = 90
c = 133.817γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and TechnologyJapanNo. 25291008

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references