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 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

  • 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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L2
A
137Geobacillus stearothermophilusGene Names: rplB
Find proteins for P04257 (Geobacillus stearothermophilus)
Go to UniProtKB:  P04257
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L6
B
177Geobacillus stearothermophilusGene Names: rplF
Find proteins for P02391 (Geobacillus stearothermophilus)
Go to UniProtKB:  P02391
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L11
C
67Geobacillus stearothermophilusGene Names: rplK
Find proteins for P56210 (Geobacillus stearothermophilus)
Go to UniProtKB:  P56210
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L14
D
122Geobacillus stearothermophilusGene Names: rplN
Find proteins for P04450 (Geobacillus stearothermophilus)
Go to UniProtKB:  P04450
Entity ID: 1
MoleculeChainsLengthOrganism
23S RRNA FRAGMENTE58Haloarcula marismortui
Entity ID: 2
MoleculeChainsLengthOrganism
23S RRNA FRAGMENTF29Haloarcula marismortui
Small Molecules
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: 5 Å
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 212.000α = 90.00
b = 301.400β = 90.00
c = 576.300γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing
Omodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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