1C04

IDENTIFICATION OF KNOWN PROTEIN AND RNA STRUCTURES IN A 5 A MAP OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit.

Ban, N.Nissen, P.Hansen, J.Capel, M.Moore, P.B.Steitz, T.A.

(1999) Nature 400: 841-847

  • DOI: 10.1038/23641
  • Primary Citation of Related Structures:  
    1C04

  • PubMed Abstract: 
  • We have calculated at 5.0 A resolution an electron-density map of the large 50S ribosomal subunit from the bacterium Haloarcula marismortui by using phases derived from four heavy-atom derivatives, intercrystal density averaging and density-modificat ...

    We have calculated at 5.0 A resolution an electron-density map of the large 50S ribosomal subunit from the bacterium Haloarcula marismortui by using phases derived from four heavy-atom derivatives, intercrystal density averaging and density-modification procedures. More than 300 base pairs of A-form RNA duplex have been fitted into this map, as have regions of non-A-form duplex, single-stranded segments and tetraloops. The long rods of RNA crisscrossing the subunit arise from the stacking of short, separate double helices, not all of which are A-form, and in many places proteins crosslink two or more of these rods. The polypeptide exit channel was marked by tungsten cluster compounds bound in one heavy-atom-derivatized crystal. We have determined the structure of the translation-factor-binding centre by fitting the crystal structures of the ribosomal proteins L6, L11 and L14, the sarcin-ricin loop RNA, and the RNA sequence that binds L11 into the electron density. We can position either elongation factor G or elongation factor Tu complexed with an aminoacylated transfer RNA and GTP onto the factor-binding centre in a manner that is consistent with results from biochemical and electron microscopy studies.


    Related Citations: 
    • A 9 A resolution X-ray crystallographic map of the large ribosomal subunit
      Ban, N., Freeborn, B., Nissen, P., Penczec, P., Grassucci, R.A., Sweet, R., Frank, J., Moore, P.B., Steitz, T.A.
      (1998) Cell 26: 1105

    Organizational Affiliation

    Department of Molecular Biophysics & Biochemistry, Yale University, Howard Hughes Medical Institute, New Haven, Connecticut 06520-8114, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L2A137Haloarcula marismortuiMutation(s): 0 
Find proteins for P04257 (Geobacillus stearothermophilus)
Explore P04257 
Go to UniProtKB:  P04257
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L6B177Haloarcula marismortuiMutation(s): 0 
Find proteins for P02391 (Geobacillus stearothermophilus)
Explore P02391 
Go to UniProtKB:  P02391
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L11C67Haloarcula marismortuiMutation(s): 0 
Find proteins for P56210 (Geobacillus stearothermophilus)
Explore P56210 
Go to UniProtKB:  P56210
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L14D122Haloarcula marismortuiMutation(s): 0 
Find proteins for P04450 (Geobacillus stearothermophilus)
Explore P04450 
Go to UniProtKB:  P04450
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
23S RRNA FRAGMENTE58Haloarcula marismortui
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
23S RRNA FRAGMENTF29Haloarcula marismortui
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212α = 90
b = 301.4β = 90
c = 576.3γ = 90
Software Package:
Software NamePurpose
CNSrefinement
Omodel building
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance