1F7Y

THE CRYSTAL STRUCTURE OF TWO UUCG LOOPS HIGHLIGHTS THE ROLE PLAYED BY 2'-HYDROXYL GROUPS IN ITS UNUSUAL STABILITY

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

The crystal structure of UUCG tetraloop.

Ennifar, E., Nikulin, A., Tishchenko, S., Serganov, A., Nevskaya, N., Garber, M., Ehresmann, B., Ehresmann, C., Nikonov, S., Dumas, P.

(2000) J Mol Biol 304: 35-42

  • DOI: https://doi.org/10.1006/jmbi.2000.4204
  • Primary Citation of Related Structures:  
    1F7Y

  • PubMed Abstract: 

    All large structured RNAs contain hairpin motifs made of a stem closed by several looped nucleotides. The most frequent loop motif is the UUCG one. This motif belongs to the tetraloop family and has the peculiarity of being highly thermodynamically stable. Here, we report the first crystal structure of two UUCG tetraloops embedded in a larger RNA-protein complex solved at 2.8 A resolution. The two loops present in the asymmetric unit are in a different crystal packing environment but, nevertheless, have an identical conformation. The observed structure is globally close to that obtained in solution by nuclear magnetic resonance. However, subtle differences point to a more detailed picture of the role played by 2'-hydroxyl groups in stabilising this tetraloop.

    • Organizational Affiliation: 

    UPR 9002 du CNRS, IBMC, 15 rue R. Descartes, 67084 Strasbourg-cedex, France.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15B [auth A]89Thermus thermophilusMutation(s): 4 
UniProt
Find proteins for P80378 (Thermus thermophilus)
Explore P80378 
Go to UniProtKB:  P80378
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80378
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RIBOSOMAL RNA FRAGMENTA [auth B]57N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download Ideal Coordinates CCD File 
N [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG
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C [auth B]
D [auth B]
E [auth B]
F [auth B]
G [auth B]
C [auth B],
D [auth B],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
L [auth B],
M [auth B]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE		B [auth A]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.8α = 90
b = 128.8β = 90
c = 65.1γ = 120
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-12-28
    Changes: Advisory
  • Version 1.4: 2021-11-03
    Changes: Data collection, Database references, Derived calculations