2PA2

Crystal structure of human Ribosomal protein L10 core domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Human Ribosomal Protein L10 Core Domain Reveals Eukaryote-Specific Motifs in Addition to the Conserved Fold

Nishimura, M.Kaminishi, T.Takemoto, C.Kawazoe, M.Yoshida, T.Tanaka, A.Sugano, S.Shirouzu, M.Ohkubo, T.Yokoyama, S.Kobayashi, Y.

(2008) J.Mol.Biol. 377: 421-430

  • DOI: 10.1016/j.jmb.2008.01.003

  • PubMed Abstract: 
  • A phylogenetically conserved ribosomal protein L16p/L10e organizes the architecture of the aminoacyl tRNA binding site on the large ribosomal subunit. Eukaryotic L10 also exhibits a variety of cellular activities, and, in particular, human L10 is kno ...

    A phylogenetically conserved ribosomal protein L16p/L10e organizes the architecture of the aminoacyl tRNA binding site on the large ribosomal subunit. Eukaryotic L10 also exhibits a variety of cellular activities, and, in particular, human L10 is known as a putative tumor suppressor, QM. We have determined the 2.5-A crystal structure of the human L10 core domain that corresponds to residues 34-182 of the full-length 214 amino acids. Its two-layered alpha+beta architecture is significantly similar to those of the archaeal and bacterial homologues, substantiating a high degree of structural conservation across the three phylogenetic domains. A cation-binding pocket formed between alpha2 and beta 6 is similar to that of the archaeal L10 protein but appears to be better ordered. Previously reported L10 mutations that cause defects in the yeast ribosome are clustered around this pocket, indicating that its integrity is crucial for its role in L10 function. Characteristic interactions among Arg90-Trp171-Arg139 guide the C-terminal part outside of the central fold, implying that the eukaryote-specific C-terminal extension localizes on the outer side of the ribosome.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
A, B
151Homo sapiensMutation(s): 0 
Gene Names: RPL10 (DXS648E, QM)
Find proteins for P27635 (Homo sapiens)
Go to Gene View: RPL10
Go to UniProtKB:  P27635
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.240 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 52.724α = 90.00
b = 52.724β = 90.00
c = 185.489γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance