5LYV

The crystal structure of 7SK 5'-hairpin - Osmium derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of the 5 functional domain of the transcription riboregulator 7SK.

Martinez-Zapien, D.Legrand, P.McEwen, A.G.Proux, F.Cragnolini, T.Pasquali, S.Dock-Bregeon, A.C.

(2017) Nucleic Acids Res. 45: 3568-3579

  • DOI: 10.1093/nar/gkw1351
  • Primary Citation of Related Structures:  5LYS, 5LYU

  • PubMed Abstract: 
  • In vertebrates, the 7SK RNA forms the scaffold of a complex, which regulates transcription pausing of RNA-polymerase II. By binding to the HEXIM protein, the complex comprising proteins LARP7 and MePCE captures the positive transcription elongation f ...

    In vertebrates, the 7SK RNA forms the scaffold of a complex, which regulates transcription pausing of RNA-polymerase II. By binding to the HEXIM protein, the complex comprising proteins LARP7 and MePCE captures the positive transcription elongation factor P-TEFb and prevents phosphorylation of pausing factors. The HEXIM-binding site embedded in the 5΄-hairpin of 7SK (HP1) encompasses a short signature sequence, a GAUC repeat framed by single-stranded uridines. The present crystal structure of HP1 shows a remarkably straight helical stack involving several unexpected triples formed at a central region. Surprisingly, two uridines of the signature sequence make triple interactions in the major groove of the (GAUC)2. The third uridine is turned outwards or inward, wedging between the other uridines, thus filling the major groove. A molecular dynamics simulation indicates that these two conformations of the signature sequence represent stable alternatives. Analyses of the interaction with the HEXIM protein confirm the importance of the triple interactions at the signature sequence. Altogether, the present structural analysis of 7SK HP1 highlights an original mechanism of swapping bases, which could represent a possible '7SK signature' and provides new insight into the functional importance of the plasticity of RNA.


    Organizational Affiliation

    Biotechnologie et signalisation cellulaire, CNRS UMR 7242, Ecole Supérieure de Biotechnologie de Strasbourg, F-67412 Illkirch, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (57-MER)A,B57Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CCC
Query on CCC

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Download CCD File 
A, B
CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
C9 H13 N3 O10 P2
IZJNKZMLZILGRK-XVFCMESISA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
OHX
Query on OHX

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Download CCD File 
A
osmium (III) hexammine
osmium(6+) hexaazanide
H12 N6 Os
OWCQTVJQFLTQTE-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CCC
Query on CCC
A, B
RNA LINKINGC9 H13 N3 O10 P2C
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.120α = 90.00
b = 47.740β = 105.20
c = 68.940γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
BUSTERrefinement
XSCALEdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
French National Research AgencyFranceANR-06-BLAN-0072
French National Research AgencyFranceANR-12-BSV5-0018
French National Research AgencyFranceANR-10-INSB-05-01

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references
  • Version 1.2: 2017-08-30
    Type: Author supporting evidence, Derived calculations