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PDBsum entry 1hq1
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Signaling protein/RNA
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PDB id
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1hq1
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle.
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Authors
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R.T.Batey,
M.B.Sagar,
J.A.Doudna.
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Ref.
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J Mol Biol, 2001,
307,
229-246.
[DOI no: ]
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PubMed id
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Abstract
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The signal recognition particle (SRP) is a ribonucleoprotein complex responsible
for targeting proteins to the endoplasmic reticulum in eukarya or to the inner
membrane in prokarya. The crystal structure of the universally conserved
RNA-protein core of the Escherichia coli SRP, refined here to 1.5 A resolution,
revealed minor groove recognition of the 4.5 S RNA component by the M domain of
the Ffh protein. Within the RNA, nucleotides comprising two phylogenetically
conserved internal loops create a unique surface for protein recognition. To
determine the energetic importance of conserved nucleotides for SRP assembly, we
measured the affinity of the M domain for a series of RNA mutants. This analysis
reveals how conserved nucleotides within the two internal loop motifs establish
the architecture of the macromolecular interface and position essential
functional groups for direct recognition by the protein.
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Figure 6.
Figure 6. Summary of the M domain-RNA interactions and
crystal contacts observed. The intermolecular contacts made by
protein and RNA that are boxed in red. Crystal contacts made by
neighboring complexes in the crystal are boxed in light blue,
purple, orange, and green, with each color representing a
physically distinct molecule. The thick broken lines between
Arg398 and A39, C40 and C41 represent stacking interactions and
blue spheres denote water-mediated interactions.
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Figure 7.
Figure 7. Tetraloop-minor groove interaction. (a) Stereo
representation of the GAAA tetraloop of one molecule interacting
with the minor groove of an adjacent RNA. (b) Base triples
formed by this contact, with the final 2F[o] - F[c] electron
density map contoured at 1.6s superimposed. The hydrogen bond
between A54 and U34 is mediated by a solvent molecule.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
307,
229-246)
copyright 2001.
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