1ZAW | pdb_00001zaw

Ribosomal Protein L10-L12(NTD) Complex, Space Group P212121, Form A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.272 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1ZAW

This is version 1.3 of the entry. See complete history

Literature

Structural Basis for the Function of the Ribosomal L7/12 Stalk in Factor Binding and GTPase Activation.

Diaconu, M.Kothe, U.Schluenzen, F.Fischer, N.Harms, J.M.Tonevitski, A.G.Stark, H.Rodnina, M.V.Wahl, M.C.

(2005) Cell 121: 991-1004

  • DOI: https://doi.org/10.1016/j.cell.2005.04.015
  • Primary Citation Related Structures: 
    1ZAV, 1ZAW, 1ZAX

  • PubMed Abstract: 

    The L7/12 stalk of the large subunit of bacterial ribosomes encompasses protein L10 and multiple copies of L7/12. We present crystal structures of Thermotoga maritima L10 in complex with three L7/12 N-terminal-domain dimers, refine the structure of an archaeal L10E N-terminal domain on the 50S subunit, and identify these elements in cryo-electron-microscopic reconstructions of Escherichia coli ribosomes. The mobile C-terminal helix alpha8 of L10 carries three L7/12 dimers in T. maritima and two in E. coli, in concordance with the different length of helix alpha8 of L10 in these organisms. The stalk is organized into three elements (stalk base, L10 helix alpha8-L7/12 N-terminal-domain complex, and L7/12 C-terminal domains) linked by flexible connections. Highly mobile L7/12 C-terminal domains promote recruitment of translation factors to the ribosome and stimulate GTP hydrolysis by the ribosome bound factors through stabilization of their active GTPase conformation.


  • Organizational Affiliation
    • Röntgenkristallographie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 41.32 kDa 
  • Atom Count: 3,041 
  • Modeled Residue Count: 353 
  • Deposited Residue Count: 360 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L10180Thermotoga maritimaMutation(s): 3 
Gene Names: rplJ
UniProt
Find proteins for P29394 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore P29394 
Go to UniProtKB:  P29394
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29394
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L7/L1230Thermotoga maritimaMutation(s): 1 
Gene Names: rplL
UniProt
Find proteins for P29396 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore P29396 
Go to UniProtKB:  P29396
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29396
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.272 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.934α = 90
b = 84.933β = 90
c = 63.939γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary