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PDBsum entry 1qzx
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Signaling protein
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PDB id
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1qzx
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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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Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication.
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Authors
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K.R.Rosendal,
K.Wild,
G.Montoya,
I.Sinning.
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Ref.
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Proc Natl Acad Sci U S A, 2003,
100,
14701-14706.
[DOI no: ]
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PubMed id
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Abstract
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Targeting of secretory and membrane proteins by the signal recognition particle
(SRP) is evolutionarily conserved, and the multidomain protein SRP54 acts as the
key player in SRP-mediated protein transport. Binding of a signal peptide to
SRP54 at the ribosome is coordinated with GTP binding and subsequent complex
formation with the SRP receptor. Because these functions are localized to
distinct domains of SRP54, communication between them is essential. We report
the crystal structures of SRP54 from the Archaeon Sulfolobus solfataricus with
and without its cognate SRP RNA binding site (helix 8) at 4-A resolution. The
two structures show the flexibility of the SRP core and the position of SRP54
relative to the RNA. A long linker helix connects the GTPase (G domain) with the
signal peptide binding (M) domain, and a hydrophobic contact between the N and M
domains relates the signal peptide binding site to the G domain. Hinge regions
are identified in the linker between the G and M domains (292-LGMGD) and in the
N-terminal part of the M domain, which allow for structural rearrangements
within SRP54 upon signal peptide binding at the ribosome.
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Figure 2.
Fig. 2. Superposition of SRP54 with (red) and without
(blue) RNA shown as a ribbon diagram. The RNA is omitted for
clarity. A rotation axis (green) has been identified between the
N and M domains by the program DYNDOM (50); the flexibility of
SRP54 is indicated by a black arrow.
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Figure 4.
Fig. 4. Structure of the proposed signal peptide binding
site. (A) Closed conformation of the hydrophobic groove in the
S. solfataricus SRP54/RNA complex. The finger loop is folded
into the groove. Helix  ML is not shown for
clarity. Elements involved in signal peptide binding are named.
(B) Superposition of the M domain of S. solfataricus (red) and
T. aquaticus (blue) to visualize the different conformations of
the signal peptide binding groove including the finger loop and
helix M1b. Movements between
structures are indicated by black arrows. The position of the
conserved motifs GP (green) and PG (pink) differ significantly,
the two "anchor" points (Leu-329 and Ile-374) are marked as
spheres. (C) Structure of the M domain of T. aquaticus Ffh with
the finger loop in an open conformation. A putative signal
peptide (gray cylinder) is modeled into the binding site. (D)
Model for the conformational changes in the SRP core. SRP54 is
shown in a ribbon diagram; color code is as in Fig. 1 A.
Rearrangements in SRP54 upon interaction with a signal peptide
at the ribosome (see text) are indicated by arrows, the linker
region LGMGD is indicated by a blue sphere, the anchor points
Leu-329 and the N terminus of helix M2 (Ile-374) as well as
the GP and PG motifs are shown as pink spheres. The M[N] domain
is adjusted at the four pink spheres to adopt a conformation
competent for signal peptide binding as shown in C. The GTP
(space-filling model) and the signal peptide (gray cylinder) are
placed in their respective binding sites.
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