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PDBsum entry 2c4z
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* Residue conservation analysis
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PDB id:
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Virus/RNA
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Title:
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Ms2-RNA hairpin (2su -5-6) complex
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Structure:
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Coat protein. Chain: a, b, c. Engineered: yes. 5'-r( Ap Cp Ap Up Gp Ap Gp Gp Ap Sur Sur Ap Cp Cp Cp Ap Up Gp U)-3'. Chain: r, s. Engineered: yes
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Source:
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Enterobacterio phage ms2. Organism_taxid: 12022. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 12022
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Resolution:
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2.60Å
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R-factor:
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0.191
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R-free:
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0.193
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Authors:
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E.Grahn,T.Moss,C.Helgstrand,K.Fridborg,M.Sundaram,K.Tars,H.Lago, N.J.Stonehouse,D.R.Davis,P.G.Stockley,L.Liljas
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Key ref:
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E.Grahn
et al.
(2001).
Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex.
Rna,
7,
1616-1627.
PubMed id:
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Date:
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25-Oct-05
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Release date:
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05-Jan-06
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Supersedes:
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PROCHECK
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Headers
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References
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P03612
(CAPSD_BPMS2) -
Capsid protein from Escherichia phage MS2
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Seq:
Struc:
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130 a.a.
129 a.a.
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Key: |
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Secondary structure |
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CATH domain |
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C-A-U-G-A-G-G-A-SUR-SUR-A-C-C-C-A-U-G
17 bases
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U-G-A-G-G-A-SUR-SUR-A-C-C-C-A
13 bases
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Rna
7:1616-1627
(2001)
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PubMed id:
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Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex.
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E.Grahn,
T.Moss,
C.Helgstrand,
K.Fridborg,
M.Sundaram,
K.Tars,
H.Lago,
N.J.Stonehouse,
D.R.Davis,
P.G.Stockley,
L.Liljas.
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ABSTRACT
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We have determined the X-ray structures of six MS2 RNA hairpin-coat-protein
complexes having five different substitutions at the hairpin loop base -5. This
is a uracil in the wild-type hairpin and contacts the coat protein both by
stacking on to a tyrosine side chain and by hydrogen bonding to an asparagine
side chain. The RNA consensus sequence derived from coat protein binding studies
with natural sequence variants suggested that the -5 base needs to be a
pyrimidine for strong binding. The five -5 substituents used in this study were
5-bromouracil, pyrimidin-2-one, 2-thiouracil, adenine, and guanine. The
structure of the 5-bromouracil complex was determined to 2.2 A resolution, which
is the highest to date for any MS2 RNA-protein complex. All the complexes
presented here show very similar conformations, despite variation in affinity in
solution. The results suggest that the stacking of the -5 base on to the
tyrosine side chain is the most important driving force for complex formation. A
number of hydrogen bonds that are present in the wild-type complex are not
crucial for binding, as they are missing in one or more of the complexes. The
results also reveal the flexibility of this RNA-protein interface, with respect
to functional group variation, and may be generally applicable to other
RNA-protein complexes.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Shulman-Peleg,
M.Shatsky,
R.Nussinov,
and
H.J.Wolfson
(2008).
Prediction of interacting single-stranded RNA bases by protein-binding patterns.
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J Mol Biol,
379,
299-316.
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J.J.Ellis,
and
S.Jones
(2008).
Evaluating conformational changes in protein structures binding RNA.
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Proteins,
70,
1518-1526.
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S.E.Aniagyei,
C.Dufort,
C.C.Kao,
and
B.Dragnea
(2008).
Self-assembly approaches to nanomaterial encapsulation in viral protein cages.
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J Mater Chem,
18,
3763-3774.
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A.Barthel,
and
M.Zacharias
(2006).
Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study.
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Biophys J,
90,
2450-2462.
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W.T.Horn,
K.Tars,
E.Grahn,
C.Helgstrand,
A.J.Baron,
H.Lago,
C.J.Adams,
D.S.Peabody,
S.E.Phillips,
N.J.Stonehouse,
L.Liljas,
and
P.G.Stockley
(2006).
Structural basis of RNA binding discrimination between bacteriophages Qbeta and MS2.
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Structure,
14,
487-495.
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PDB codes:
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W.T.Horn,
M.A.Convery,
N.J.Stonehouse,
C.J.Adams,
L.Liljas,
S.E.Phillips,
and
P.G.Stockley
(2004).
The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions.
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RNA,
10,
1776-1782.
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PDB code:
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C.Helgstrand,
E.Grahn,
T.Moss,
N.J.Stonehouse,
K.Tars,
P.G.Stockley,
and
L.Liljas
(2002).
Investigating the structural basis of purine specificity in the structures of MS2 coat protein RNA translational operator hairpins.
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Nucleic Acids Res,
30,
2678-2685.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
