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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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Contents |
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* Residue conservation analysis
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PDB id:
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Nucleotide-binding
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Title:
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Model for eef3 bound to an 80s ribosome
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Structure:
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Elongation factor 3a. Chain: a. Fragment: residues 1-976. Synonym: ef-3a, ef-3, translation elongation factor 3a, eukaryotic elongation factor 3, eef3, yeast elongation factor 3. Engineered: yes. Other_details: translation elongation in fungi abc-type atpase tRNA release
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Source:
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Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
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Authors:
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C.B.F.Andersen,T.Becker,M.Blau,M.Anand,M.Halic,B.Balar,T.Mielke, T.Boesen,J.S.Pedersen,C.M.T.Spahn,T.G.Kinzy,G.R.Andersen,R.Beckmann
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Key ref:
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C.B.Andersen
et al.
(2006).
Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
Nature,
443,
663-668.
PubMed id:
DOI:
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Date:
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07-Jul-06
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Release date:
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10-Jul-07
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PROCHECK
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Headers
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References
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P16521
(EF3A_YEAST) -
Elongation factor 3A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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Seq:
Struc:
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1044 a.a.
976 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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*
PDB and UniProt seqs differ
at 2 residue positions (black
crosses)
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DOI no:
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Nature
443:663-668
(2006)
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PubMed id:
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Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
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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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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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Selected figure(s)
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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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Figures were
selected
by an automated process.
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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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I.Holdermann,
N.H.Meyer,
A.Round,
K.Wild,
M.Sattler,
and
I.Sinning
(2012).
Chromodomains read the arginine code of post-translational targeting.
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Nat Struct Mol Biol,
19,
260-263.
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PDB code:
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A.Ben-Shem,
L.Jenner,
G.Yusupova,
and
M.Yusupov
(2010).
Crystal structure of the eukaryotic ribosome.
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Science,
330,
1203-1209.
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PDB codes:
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A.V.Pisarev,
M.A.Skabkin,
V.P.Pisareva,
O.V.Skabkina,
A.M.Rakotondrafara,
M.W.Hentze,
C.U.Hellen,
and
T.V.Pestova
(2010).
The role of ABCE1 in eukaryotic posttermination ribosomal recycling.
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Mol Cell,
37,
196-210.
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J.B.Munro,
R.B.Altman,
C.S.Tung,
K.Y.Sanbonmatsu,
and
S.C.Blanchard
(2010).
A fast dynamic mode of the EF-G-bound ribosome.
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EMBO J,
29,
770-781.
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J.P.Armache,
A.Jarasch,
A.M.Anger,
E.Villa,
T.Becker,
S.Bhushan,
F.Jossinet,
M.Habeck,
G.Dindar,
S.Franckenberg,
V.Marquez,
T.Mielke,
M.Thomm,
O.Berninghausen,
B.Beatrix,
J.Söding,
E.Westhof,
D.N.Wilson,
and
R.Beckmann
(2010).
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
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Proc Natl Acad Sci U S A,
107,
19754-19759.
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PDB codes:
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S.Kurata,
K.H.Nielsen,
S.F.Mitchell,
J.R.Lorsch,
A.Kaji,
and
H.Kaji
(2010).
Ribosome recycling step in yeast cytoplasmic protein synthesis is catalyzed by eEF3 and ATP.
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Proc Natl Acad Sci U S A,
107,
10854-10859.
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J.D.Dinman
(2009).
The eukaryotic ribosome: current status and challenges.
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J Biol Chem,
284,
11761-11765.
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J.Timmins,
E.Gordon,
S.Caria,
G.Leonard,
S.Acajjaoui,
M.S.Kuo,
V.Monchois,
and
S.McSweeney
(2009).
Structural and mutational analyses of Deinococcus radiodurans UvrA2 provide insight into DNA binding and damage recognition by UvrAs.
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Structure,
17,
547-558.
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PDB codes:
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K.Vu,
J.Bautos,
M.P.Hong,
and
A.Gelli
(2009).
The functional expression of toxic genes: lessons learned from molecular cloning of CCH1, a high-affinity Ca2+ channel.
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Anal Biochem,
393,
234-241.
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N.Van Dyke,
B.F.Pickering,
and
M.W.Van Dyke
(2009).
Stm1p alters the ribosome association of eukaryotic elongation factor 3 and affects translation elongation.
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Nucleic Acids Res,
37,
6116-6125.
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S.Paytubi,
X.Wang,
Y.W.Lam,
L.Izquierdo,
M.J.Hunter,
E.Jan,
H.S.Hundal,
and
C.G.Proud
(2009).
ABC50 promotes translation initiation in mammalian cells.
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J Biol Chem,
284,
24061-24073.
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A.Karcher,
A.Schele,
and
K.P.Hopfner
(2008).
X-ray structure of the complete ABC enzyme ABCE1 from Pyrococcus abyssi.
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J Biol Chem,
283,
7962-7971.
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PDB code:
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A.L.Davidson,
E.Dassa,
C.Orelle,
and
J.Chen
(2008).
Structure, function, and evolution of bacterial ATP-binding cassette systems.
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Microbiol Mol Biol Rev,
72,
317.
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J.Botet,
M.Rodríguez-Mateos,
J.P.Ballesta,
J.L.Revuelta,
and
M.Remacha
(2008).
A chemical genomic screen in Saccharomyces cerevisiae reveals a role for diphthamidation of translation elongation factor 2 in inhibition of protein synthesis by sordarin.
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Antimicrob Agents Chemother,
52,
1623-1629.
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J.LeBarron,
R.A.Grassucci,
T.R.Shaikh,
W.T.Baxter,
J.Sengupta,
and
J.Frank
(2008).
Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.
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J Struct Biol,
164,
24-32.
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M.Liu,
and
A.Gelli
(2008).
Elongation factor 3, EF3, associates with the calcium channel Cch1 and targets Cch1 to the plasma membrane in Cryptococcus neoformans.
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Eukaryot Cell,
7,
1118-1126.
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M.V.Petoukhov,
J.B.Vicente,
P.B.Crowley,
M.A.Carrondo,
M.Teixeira,
and
D.I.Svergun
(2008).
Quaternary structure of flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering.
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Structure,
16,
1428-1436.
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P.Chandramouli,
M.Topf,
J.F.Ménétret,
N.Eswar,
J.J.Cannone,
R.R.Gutell,
A.Sali,
and
C.W.Akey
(2008).
Structure of the mammalian 80S ribosome at 8.7 A resolution.
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Structure,
16,
535-548.
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PDB codes:
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T.V.Budkevich,
A.V.El'skaya,
and
K.H.Nierhaus
(2008).
Features of 80S mammalian ribosome and its subunits.
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Nucleic Acids Res,
36,
4736-4744.
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V.Di Giacco,
V.Márquez,
Y.Qin,
M.Pech,
F.J.Triana-Alonso,
D.N.Wilson,
and
K.H.Nierhaus
(2008).
Shine-Dalgarno interaction prevents incorporation of noncognate amino acids at the codon following the AUG.
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Proc Natl Acad Sci U S A,
105,
10715-10720.
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E.P.Plant,
P.Nguyen,
J.R.Russ,
Y.R.Pittman,
T.Nguyen,
J.T.Quesinberry,
T.G.Kinzy,
and
J.D.Dinman
(2007).
Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae.
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PLoS ONE,
2,
e517.
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O.Galkin,
A.A.Bentley,
S.Gupta,
B.A.Compton,
B.Mazumder,
T.G.Kinzy,
W.C.Merrick,
M.Hatzoglou,
T.V.Pestova,
C.U.Hellen,
and
A.A.Komar
(2007).
Roles of the negatively charged N-terminal extension of Saccharomyces cerevisiae ribosomal protein S5 revealed by characterization of a yeast strain containing human ribosomal protein S5.
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RNA,
13,
2116-2128.
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V.Berk,
and
J.H.Cate
(2007).
Insights into protein biosynthesis from structures of bacterial ribosomes.
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Curr Opin Struct Biol,
17,
302-309.
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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
code is
shown on the right.
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Links
