1MMS

Crystal structure of the ribosomal PROTEIN L11-RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A detailed view of a ribosomal active site: the structure of the L11-RNA complex.

Wimberly, B.T.Guymon, R.McCutcheon, J.P.White, S.W.Ramakrishnan, V.

(1999) Cell 97: 491-502

  • DOI: https://doi.org/10.1016/s0092-8674(00)80759-x
  • Primary Citation of Related Structures:  
    1MMS

  • PubMed Abstract: 

    We report the crystal structure of a 58 nucleotide fragment of 23S ribosomal RNA bound to ribosomal protein L11. This highly conserved ribonucleoprotein domain is the target for the thiostrepton family of antibiotics that disrupt elongation factor function. The highly compact RNA has both familiar and novel structural motifs. While the C-terminal domain of L11 binds RNA tightly, the N-terminal domain makes only limited contacts with RNA and is proposed to function as a switch that reversibly associates with an adjacent region of RNA. The sites of mutations conferring resistance to thiostrepton and micrococcin line a narrow cleft between the RNA and the N-terminal domain. These antibiotics are proposed to bind in this cleft, locking the putative switch and interfering with the function of elongation factors.


  • Organizational Affiliation

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City 84132, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (RIBOSOMAL PROTEIN L11)C [auth A],
D [auth B]
140Thermotoga maritimaMutation(s): 0 
UniProt
Find proteins for P29395 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore P29395 
Go to UniProtKB:  P29395
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29395
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
23S RIBOSOMAL RNAA [auth C],
B [auth D]
58N/A
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MMC
Query on MMC

Download Ideal Coordinates CCD File 
EA [auth D]
FA [auth D]
GA [auth D]
KA [auth A]
LA [auth A]
EA [auth D],
FA [auth D],
GA [auth D],
KA [auth A],
LA [auth A],
MA [auth A],
Q [auth C],
R [auth C]
METHYL MERCURY ION
C H3 Hg
DBUXSCUEGJMZAE-UHFFFAOYSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
CA [auth D]
E [auth C]
F [auth C]
H [auth C]
IA [auth A]
CA [auth D],
E [auth C],
F [auth C],
H [auth C],
IA [auth A],
JA [auth A],
S [auth D],
T [auth D]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
DA [auth D]
G [auth C]
HA [auth A]
AA [auth D],
BA [auth D],
DA [auth D],
G [auth C],
HA [auth A],
I [auth C],
J [auth C],
K [auth C],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
U [auth D],
V [auth D],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.89α = 90
b = 84.26β = 90
c = 155.51γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-17
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-27
    Changes: Database references
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations