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PDBsum entry 2ix8
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Nucleotide-binding
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PDB id
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2ix8
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References listed in PDB file
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Key reference
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Title
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Structure of eef3 and the mechanism of transfer RNA release from the e-Site.
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Authors
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C.B.Andersen,
T.Becker,
M.Blau,
M.Anand,
M.Halic,
B.Balar,
T.Mielke,
T.Boesen,
J.S.Pedersen,
C.M.Spahn,
T.G.Kinzy,
G.R.Andersen,
R.Beckmann.
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Ref.
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Nature, 2006,
443,
663-668.
[DOI no: ]
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PubMed id
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Abstract
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Elongation factor eEF3 is an ATPase that, in addition to the two canonical
factors eEF1A and eEF2, serves an essential function in the translation cycle of
fungi. eEF3 is required for the binding of the aminoacyl-tRNA-eEF1A-GTP ternary
complex to the ribosomal A-site and has been suggested to facilitate the
clearance of deacyl-tRNA from the E-site. Here we present the crystal structure
of Saccharomyces cerevisiae eEF3, showing that it consists of an amino-terminal
HEAT repeat domain, followed by a four-helix bundle and two ABC-type ATPase
domains, with a chromodomain inserted in ABC2. Moreover, we present the
cryo-electron microscopy structure of the ATP-bound form of eEF3 in complex with
the post-translocational-state 80S ribosome from yeast. eEF3 uses an entirely
new factor binding site near the ribosomal E-site, with the chromodomain likely
to stabilize the ribosomal L1 stalk in an open conformation, thus allowing tRNA
release.
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Figure 1.
Figure 1: Structures of Saccharomyces cerevisiae eEF3 and
nucleotide binding. a, Schematic representation of the
eEF3 sequence. See the text for a description of the different
domains. Chromo, chromodomain; C-term, carboxy-terminal domain.
b, Stereo view of the crystal structure of eEF3–ADP. The
nucleotide is shown in ball-and-stick representation. c, Stereo
view of the nucleotide-binding site. The electron density of ADP
is generated from an omit map contoured at 1.5  (grey)
or at 0.8 around
the  -phosphate
(green). d, Three different conformations of eEF3. Left: crystal
structure of eEF3. Middle: ATP model of eEF3 constructed using
homology to the structure of MJ0796. Right: Cryo-electron
microscopy (cryo-EM) reconstruction of eEF3 on the 80S ribosome.
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Figure 4.
Figure 4: Model of the role of eEF3 in the fungal elongation
cycle. a, The post-state ribosome with a locked E-site tRNA
owing to the L1 stalk in the 'in' position and the conformation
of the 40S head (Post, locked E). b, Hypothetical initial
interaction of eEF3 in the open tandem or intermediate
conformation (Post*, locked E). c, Ribosome interaction triggers
the ATP-dependent closed tandem formation and high-affinity
ribosome binding by eEF3, as observed by cryo-EM (Post*). A
conformational switch of the chromodomain stabilizes the L1
stalk in the 'out' position (unlocked E). d, ATP hydrolysis of
the closed tandem results in the dissociation of eEF3, E-site
opening, and unlocking of the 40S head (Post). Now,
eEF1A–GTP–aminoacyl-tRNA can bind and the E-site deacyl-tRNA
is released. ATP hydrolysis by eEF3, tRNA release, and A-site
loading by eEF1A may take place as a joint event. aatRNA,
aminoacyl-tRNA. RSR, ratchet-like subunit rearrangement.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2006,
443,
663-668)
copyright 2006.
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