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PDBsum entry 2bcw
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65 a.a.*
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68 a.a.*
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58 a.a.*
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* C-alpha coords only
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References listed in PDB file
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Key reference
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Title
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Interaction of the g' Domain of elongation factor g and the c-Terminal domain of ribosomal protein l7/l12 during translocation as revealed by cryo-Em.
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Authors
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P.P.Datta,
M.R.Sharma,
L.Qi,
J.Frank,
R.K.Agrawal.
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Ref.
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Mol Cell, 2005,
20,
723-731.
[DOI no: ]
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PubMed id
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Abstract
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During tRNA translocation on the ribosome, an arc-like connection (ALC) is
formed between the G' domain of elongation factor G (EF-G) and the L7/L12-stalk
base of the large ribosomal subunit in the GDP state. To delineate the boundary
of EF-G within the ALC, we tagged an amino acid residue near the tip of the G'
domain of EF-G with undecagold, which was then visualized with three-dimensional
cryo-electron microscopy (cryo-EM). Two distinct positions for the undecagold,
observed in the GTP-state and GDP-state cryo-EM maps of the ribosome bound EF-G,
allowed us to determine the movement of the labeled amino acid. Molecular
analyses of the cryo-EM maps show: (1) that three structural components, the
N-terminal domain of ribosomal protein L11, the C-terminal domain of ribosomal
protein L7/L12, and the G' domain of EF-G, participate in formation of the ALC;
and (2) that both EF-G and the ribosomal protein L7/L12 undergo large
conformational changes to form the ALC.
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Figure 2.
Figure 2. Localization of Amino Acid 209C in EF-G
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Figure 3.
Figure 3. Participation of EF-G in ALC Formation
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The above figures are
reprinted
by permission from Cell Press:
Mol Cell
(2005,
20,
723-731)
copyright 2005.
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Secondary reference #1
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Title
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A detailed view of a ribosomal active site: the structure of the l11-Rna complex.
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Authors
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B.T.Wimberly,
R.Guymon,
J.P.Mccutcheon,
S.W.White,
V.Ramakrishnan.
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Ref.
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Cell, 1999,
97,
491-502.
[DOI no: ]
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PubMed id
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Figure 5.
Figure 5. Protein–RNA Recognition within the
GTPase-Associated Region from Thermotoga maritima(A) Schematic
of RNA–CTD interactions observed in the crystal structure.
Unusual RNA conformational features are also indicated (see
inset for key). The color coding is the same used in the other
figures. Water molecules that mediate protein–RNA interactions
are indicated in red.(B) Detail of the recognition of the
conserved long-range A1088–U1060 pair by conserved L11
residues Gly-130 and Thr-131 from helix 5 and by the N terminus
of helix 3. (B) was made with MOLSCRIPT ([25]).
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Figure 6.
Figure 6. The Putative Thiostrepton/Micrococcin–Binding
Site in the GTPase-Associated RegionThe sites of mutations
conferring resistance to thiostrepton and micrococcin are
clustered around a cleft between the RNA and the proline-rich
helix in the L11 N-terminal domain. Residues implicated in
thiostrepton binding (A1067, A1095, and Pro-22) are highlighted
in red and labeled. The position of Tyr-61, which is protected
by thiostrepton in protein footprinting experiments, is also
indicated. Other residues highlighted in red are those that
confer micrococcin resistance (see text for details). The figure
was made with RIBBONS ([5]).
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #2
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Title
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Structure of the c-Terminal domain of the ribosomal protein l7/l12 from escherichia coli at 1.7 a.
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Authors
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M.Leijonmarck,
A.Liljas.
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Ref.
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J Mol Biol, 1987,
195,
555-579.
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PubMed id
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Secondary reference #3
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Title
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Three-Dimensional structure of the ribosomal translocase: elongation factor g from thermus thermophilus.
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Authors
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A.Aevarsson,
E.Brazhnikov,
M.Garber,
J.Zheltonosova,
Y.Chirgadze,
S.Al-Karadaghi,
L.A.Svensson,
A.Liljas.
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Ref.
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Embo J, 1994,
13,
3669-3677.
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PubMed id
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Figure 1.
Fig. 1. (A) Schematic drawing of the structure of Tthermophilus EF-G in the
absence of a guanine nucleotide. The different domains are coloured
differently. The G domain consists of two different subdomains shown
in different colours: violet for the core domain and blue for the G'
subdomain. Domain II is shown in yellow, III in orange, IV in red and
V in pink. The crystallographic model contains -90% of the residues,
the rest being poorly or not visible in the electron density maps,
most notably in domain III. The missing regions are indicated by
dashed lines. The drawing was generated with the program MOLSCRIPT
(Kraulis, 1991). (B) An overview of the domain topology and
designation of secondary structure elements within each of the five
domains. 5l-Strands are shown as triangles and helices as circles in
the wiring diagrams. f5-Strands are named by figures, helices are
named by capital letters. The naming of the different elements is in
keeping with the one used for the EF-G-GDP structure (Czworkowski et
at., 1994). The shaded elements in the G domain and domain II indicate
the structural similarity to EF-Tu. The shaded core domain of the 6
domain corresponds to the consensus GTPase fold with the conserved
sequence elements for nucleotide binding. The G' subdomain is unique
for EF-G. Owing to poor electron density, the structural model and
topology of domain III are ambiguous, but it probably has the same
topology as domain V.
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Figure 4.
Fig. 4. (A) The G domain in EF-G shown in stereo with emphasis on the unique G' shown in blue. The core of the G domain is shown
in purple and corresponds to the consensus GTPase fold with conserved sequence elements shown in red and marked GI -G4. The 'fingers' of the
G' subdomain touch the loops with consensus elements G3 (Asn-Lys-x-Asp) and G4 (Ser-Ala-Leu/Lys). The specific contact regions of the core
coincide with regions found to be for interactions with GEFs in other GTPases (Boume et al., 1991; Hwang et al., 1992; Noel et al.,
1993), suggesting that the G' subdomain functions as GEF. (B) A general functional cycle for GTPases. The three general states are the active GTP
state, the GDP state and the empty state (Boume et al., 1991). The interaction with GAPs and/or GEFs induces additional states or
conformations like the GTPase state (Liljas, 1990), leading to GTP hydrolysis upon binding to GAP. The active GTPase interacts with the effector
which may be identical to the GAP or different. GEF may not dissociate until GTP is bound (Boguski and McCormick, 1993), and more
complicated interactions between GTPase and GEF may exist (Kaziro et al., 1991). (C) The functional cycle for EF-G. This cycle deviates from the
general cycle by the absence of a GEF to facilitate the exchange of nucleotides. The G' subdomain may function as intrinsic GEF, making EF-G
able to take a 'shortcut' in the functional cycle. Similarly, transducin can go directly between the GTP state and the GDP state of the cycle since
has a large insert in the G domain (see Figure 2B), making a separate domain probably functioning as GAP (Noel et al., 1993).
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by Macmillan Publishers Ltd
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Headers
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