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 

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This is version 1.3 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: 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 ...

    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.

    Related Citations: 
    • Cooperative interactions of RNA and thiostrepton antibiotic with two domains of ribosomal protein L11.
      Xing, Y., Draper, D.E.
      (1996) Biochemistry 35: 1581
    • Site of action of a ribosomal RNA methylase conferring resistance to thiostrepton.
      Thompson, J., Schmidt, F., Cundliffe, E.
      (1982) J Biol Chem 257: 7915
    • Binding of thiostrepton to a complex of 23-S rRNA with ribosomal protein L11.
      Thompson, J., Cundliffe, E., Stark, M.
      (1979) Eur J Biochem 98: 261
    Organizational Affiliation: 

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



Macromolecules

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Entity ID: 2
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNAA [auth C],
B [auth D]		58N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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		 Ligand Interaction
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		 Ligand Interaction
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		 Ligand Interaction
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