1MZP

Structure of the L1 protuberance in the ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the L1 protuberance in the ribosome.

Nikulin, A.Eliseikina, I.Tishchenko, S.Nevskaya, N.Davydova, N.Platonova, O.Piendl, W.Selmer, M.Liljas, A.Drygin, D.Zimmermann, R.Garber, M.Nikonov, S.

(2003) Nat.Struct.Mol.Biol. 10: 104-108

  • DOI: 10.1038/nsb886

  • PubMed Abstract: 
  • The L1 protuberance of the 50S ribosomal subunit is implicated in the release/disposal of deacylated tRNA from the E site. The apparent mobility of this ribosomal region has thus far prevented an accurate determination of its three-dimensional struct ...

    The L1 protuberance of the 50S ribosomal subunit is implicated in the release/disposal of deacylated tRNA from the E site. The apparent mobility of this ribosomal region has thus far prevented an accurate determination of its three-dimensional structure within either the 50S subunit or the 70S ribosome. Here we report the crystal structure at 2.65 A resolution of ribosomal protein L1 from Sulfolobus acidocaldarius in complex with a specific 55-nucleotide fragment of 23S rRNA from Thermus thermophilus. This structure fills a major gap in current models of the 50S ribosomal subunit. The conformations of L1 and of the rRNA fragment differ dramatically from those within the crystallographic model of the T. thermophilus 70S ribosome. Incorporation of the L1-rRNA complex into the structural models of the T. thermophilus 70S ribosome and the Deinococcus radiodurans 50S subunit gives a reliable representation of most of the L1 protuberance within the ribosome.


    Organizational Affiliation

    Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50s ribosomal protein L1P
A
217Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)Mutation(s): 0 
Gene Names: rpl1
Find proteins for P35024 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Go to UniProtKB:  P35024
Entity ID: 1
MoleculeChainsLengthOrganism
fragment of 23S rRNAB55N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.219 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 156.010α = 90.00
b = 156.010β = 90.00
c = 90.429γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-21
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance