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PDBsum entry 1ipc
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RNA binding protein
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PDB id
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1ipc
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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RNA binding protein
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Title:
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Crystal structure of eukaryotic initiation factor 4e complexed with 7- methyl gtp
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Structure:
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Eukaryotic translation initiation factor 4e. Chain: a. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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2.00Å
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R-factor:
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0.192
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R-free:
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0.228
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Authors:
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K.Tomoo,X.Shen,K.Okabe,Y.Nozoe,S.Fukuhara,S.Morino,T.Ishida, T.Taniguchi,H.Hasegawa,A.Terashima,M.Sasaki,Y.Katsuya,K.Kitamura, H.Miyoshi,M.Ishikawa,K.Miura
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Key ref:
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K.Tomoo
et al.
(2002).
Crystal structures of 7-methylguanosine 5'-triphosphate (m(7)GTP)- and P(1)-7-methylguanosine-P(3)-adenosine-5',5'-triphosphate (m(7)GpppA)-bound human full-length eukaryotic initiation factor 4E: biological importance of the C-terminal flexible region.
Biochem J,
362,
539-544.
PubMed id:
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Date:
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08-May-01
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Release date:
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08-May-02
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PROCHECK
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Headers
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References
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P06730
(IF4E_HUMAN) -
Eukaryotic translation initiation factor 4E from Homo sapiens
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Seq:
Struc:
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217 a.a.
186 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Biochem J
362:539-544
(2002)
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PubMed id:
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Crystal structures of 7-methylguanosine 5'-triphosphate (m(7)GTP)- and P(1)-7-methylguanosine-P(3)-adenosine-5',5'-triphosphate (m(7)GpppA)-bound human full-length eukaryotic initiation factor 4E: biological importance of the C-terminal flexible region.
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K.Tomoo,
X.Shen,
K.Okabe,
Y.Nozoe,
S.Fukuhara,
S.Morino,
T.Ishida,
T.Taniguchi,
H.Hasegawa,
A.Terashima,
M.Sasaki,
Y.Katsuya,
K.Kitamura,
H.Miyoshi,
M.Ishikawa,
K.Miura.
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ABSTRACT
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The crystal structures of the full-length human eukaryotic initiation factor
(eIF) 4E complexed with two mRNA cap analogues [7-methylguanosine
5'-triphosphate (m(7)GTP) and
P(1)-7-methylguanosine-P(3)-adenosine-5',5'-triphosphate (m(7)GpppA)] were
determined at 2.0 A resolution (where 1 A=0.1 nm). The flexibility of the
C-terminal loop region of eIF4E complexed with m(7)GTP was significantly reduced
when complexed with m(7)GpppA, suggesting the importance of the second
nucleotide in the mRNA cap structure for the biological function of eIF4E,
especially the fixation and orientation of the C-terminal loop region, including
the eIF4E phosphorylation residue. The present results provide the structural
basis for the biological function of both N- and C-terminal mobile regions of
eIF4E in translation initiation, especially the regulatory function through the
switch-on/off of eIF4E-binding protein-eIF4E phosphorylation.
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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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K.Ruszczyńska-Bartnik,
M.Maciejczyk,
and
R.Stolarski
(2011).
Dynamical insight into Caenorhabditis elegans eIF4E recognition specificity for mono-and trimethylated structures of mRNA 5' cap.
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J Mol Model,
17,
727-737.
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D.R.Schoenberg,
and
L.E.Maquat
(2009).
Re-capping the message.
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Trends Biochem Sci,
34,
435-442.
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H.Okade,
Y.Fujita,
S.Miyamoto,
K.Tomoo,
S.Muto,
H.Miyoshi,
T.Natsuaki,
R.E.Rhoads,
and
T.Ishida
(2009).
Turnip mosaic virus genome-linked protein VPg binds C-terminal region of cap-bound initiation factor 4E orthologue without exhibiting host cellular specificity.
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J Biochem,
145,
299-307.
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H.Sato,
and
L.E.Maquat
(2009).
Remodeling of the pioneer translation initiation complex involves translation and the karyopherin importin beta.
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Genes Dev,
23,
2537-2550.
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N.M.Kaye,
K.J.Emmett,
W.C.Merrick,
and
E.Jankowsky
(2009).
Intrinsic RNA binding by the eukaryotic initiation factor 4F depends on a minimal RNA length but not on the m7G cap.
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J Biol Chem,
284,
17742-17750.
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R.E.Rhoads
(2009).
eIF4E: New Family Members, New Binding Partners, New Roles.
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J Biol Chem,
284,
16711-16715.
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R.Tuteja
(2009).
Identification and bioinformatics characterization of translation initiation complex eIF4F components and poly(A)-binding protein from Plasmodium falciparum.
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Commun Integr Biol,
2,
245-260.
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T.Ishida
(2009).
Structural studies of specific intermolecular interactions and self-aggregation of biomolecules and their application to drug design.
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Chem Pharm Bull (Tokyo),
57,
1309-1334.
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W.Liu,
R.Zhao,
C.McFarland,
J.Kieft,
A.Niedzwiecka,
M.Jankowska-Anyszka,
J.Stepinski,
E.Darzynkiewicz,
D.N.Jones,
and
R.E.Davis
(2009).
Structural insights into parasite eIF4E binding specificity for m7G and m2,2,7G mRNA caps.
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J Biol Chem,
284,
31336-31349.
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PDB codes:
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Z.Wang,
K.Treder,
and
W.A.Miller
(2009).
Structure of a Viral Cap-independent Translation Element That Functions via High Affinity Binding to the eIF4E Subunit of eIF4F.
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J Biol Chem,
284,
14189-14202.
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P.Ghosh,
J.Cheng,
T.F.Chou,
Y.Jia,
S.Avdulov,
P.B.Bitterman,
V.A.Polunovsky,
and
C.R.Wagner
(2008).
Expression, purification and characterization of recombinant mouse translation initiation factor eIF4E as a dihydrofolate reductase (DHFR) fusion protein.
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Protein Expr Purif,
60,
132-139.
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R.Worch,
and
R.Stolarski
(2008).
Stacking efficiency and flexibility analysis of aromatic amino acids in cap-binding proteins.
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Proteins,
71,
2026-2037.
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B.Kierdaszuk,
and
J.Włodarczyk
(2007).
Interpretation of fluorescence decay kinetics in 3-methylbenzimidazolyl(5'-5')guanosine dinucleotides: exponential dependence on the number of phosphates in the polyphosphate bridge.
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Eur Biophys J,
36,
253-259.
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C.Nieto,
F.Piron,
M.Dalmais,
C.F.Marco,
E.Moriones,
M.L.Gómez-Guillamón,
V.Truniger,
P.Gómez,
J.Garcia-Mas,
M.A.Aranda,
and
A.Bendahmane
(2007).
EcoTILLING for the identification of allelic variants of melon eIF4E, a factor that controls virus susceptibility.
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BMC Plant Biol,
7,
34.
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P.Nilsson,
N.Henriksson,
A.Niedzwiecka,
N.A.Balatsos,
K.Kokkoris,
J.Eriksson,
and
A.Virtanen
(2007).
A multifunctional RNA recognition motif in poly(A)-specific ribonuclease with cap and poly(A) binding properties.
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J Biol Chem,
282,
32902-32911.
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B.Kierdaszuk,
and
J.Włodarczyk
(2006).
Interpretation of intramolecular stacking effect on the fluorescence intensity decay of 3-methylbenzimidazolyl(5'-5')guanosine dinucleotides using a model of lifetime distribution.
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Eur Biophys J,
35,
424-430.
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C.Nieto,
M.Morales,
G.Orjeda,
C.Clepet,
A.Monfort,
B.Sturbois,
P.Puigdomènech,
M.Pitrat,
M.Caboche,
C.Dogimont,
J.Garcia-Mas,
M.A.Aranda,
and
A.Bendahmane
(2006).
An eIF4E allele confers resistance to an uncapped and non-polyadenylated RNA virus in melon.
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Plant J,
48,
452-462.
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L.Volpon,
M.J.Osborne,
I.Topisirovic,
N.Siddiqui,
and
K.L.Borden
(2006).
Cap-free structure of eIF4E suggests a basis for conformational regulation by its ligands.
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EMBO J,
25,
5138-5149.
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PDB code:
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T.Murata,
and
K.Shimotohno
(2006).
Ubiquitination and proteasome-dependent degradation of human eukaryotic translation initiation factor 4E.
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J Biol Chem,
281,
20788-20800.
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B.Joshi,
K.Lee,
D.L.Maeder,
and
R.Jagus
(2005).
Phylogenetic analysis of eIF4E-family members.
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BMC Evol Biol,
5,
48.
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E.Bitto,
C.A.Bingman,
H.Robinson,
S.T.Allard,
G.E.Wesenberg,
and
G.N.Phillips
(2005).
The structure at 2.5 A resolution of human basophilic leukemia-expressed protein BLES03.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
812-817.
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PDB code:
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L.Li,
and
C.C.Wang
(2005).
Identification in the ancient protist Giardia lamblia of two eukaryotic translation initiation factor 4E homologues with distinctive functions.
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Eukaryot Cell,
4,
948-959.
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R.Worch,
A.Niedzwiecka,
J.Stepinski,
C.Mazza,
M.Jankowska-Anyszka,
E.Darzynkiewicz,
S.Cusack,
and
R.Stolarski
(2005).
Specificity of recognition of mRNA 5' cap by human nuclear cap-binding complex.
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RNA,
11,
1355-1363.
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T.D.Dinkova,
B.D.Keiper,
N.L.Korneeva,
E.J.Aamodt,
and
R.E.Rhoads
(2005).
Translation of a small subset of Caenorhabditis elegans mRNAs is dependent on a specific eukaryotic translation initiation factor 4E isoform.
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Mol Cell Biol,
25,
100-113.
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B.Joshi,
A.Cameron,
and
R.Jagus
(2004).
Characterization of mammalian eIF4E-family members.
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Eur J Biochem,
271,
2189-2203.
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E.Grudzien,
J.Stepinski,
M.Jankowska-Anyszka,
R.Stolarski,
E.Darzynkiewicz,
and
R.E.Rhoads
(2004).
Novel cap analogs for in vitro synthesis of mRNAs with high translational efficiency.
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RNA,
10,
1479-1487.
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J.L.Cowan,
and
S.J.Morley
(2004).
The proteasome inhibitor, MG132, promotes the reprogramming of translation in C2C12 myoblasts and facilitates the association of hsp25 with the eIF4F complex.
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Eur J Biochem,
271,
3596-3611.
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L.D.Kapp,
and
J.R.Lorsch
(2004).
The molecular mechanics of eukaryotic translation.
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Annu Rev Biochem,
73,
657-704.
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R.Cuesta,
Q.Xi,
and
R.J.Schneider
(2004).
Structural basis for competitive inhibition of eIF4G-Mnk1 interaction by the adenovirus 100-kilodalton protein.
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J Virol,
78,
7707-7716.
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S.Lall,
C.C.Friedman,
M.Jankowska-Anyszka,
J.Stepinski,
E.Darzynkiewicz,
and
R.E.Davis
(2004).
Contribution of trans-splicing, 5' -leader length, cap-poly(A) synergism, and initiation factors to nematode translation in an Ascaris suum embryo cell-free system.
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J Biol Chem,
279,
45573-45585.
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T.Ueda,
R.Watanabe-Fukunaga,
H.Fukuyama,
S.Nagata,
and
R.Fukunaga
(2004).
Mnk2 and Mnk1 are essential for constitutive and inducible phosphorylation of eukaryotic initiation factor 4E but not for cell growth or development.
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Mol Cell Biol,
24,
6539-6549.
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Z.Gao,
E.Johansen,
S.Eyers,
C.L.Thomas,
T.H.Noel Ellis,
and
A.J.Maule
(2004).
The potyvirus recessive resistance gene, sbm1, identifies a novel role for translation initiation factor eIF4E in cell-to-cell trafficking.
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Plant J,
40,
376-385.
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J.Jemielity,
T.Fowler,
J.Zuberek,
J.Stepinski,
M.Lewdorowicz,
A.Niedzwiecka,
R.Stolarski,
E.Darzynkiewicz,
and
R.E.Rhoads
(2003).
Novel "anti-reverse" cap analogs with superior translational properties.
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RNA,
9,
1108-1122.
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J.Zuberek,
A.Wyslouch-Cieszynska,
A.Niedzwiecka,
M.Dadlez,
J.Stepinski,
W.Augustyniak,
A.C.Gingras,
Z.Zhang,
S.K.Burley,
N.Sonenberg,
R.Stolarski,
and
E.Darzynkiewicz
(2003).
Phosphorylation of eIF4E attenuates its interaction with mRNA 5' cap analogs by electrostatic repulsion: intein-mediated protein ligation strategy to obtain phosphorylated protein.
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RNA,
9,
52-61.
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K.Ruszczynska,
K.Kamienska-Trela,
J.Wojcik,
J.Stepinski,
E.Darzynkiewicz,
and
R.Stolarski
(2003).
Charge distribution in 7-methylguanine regarding cation-pi interaction with protein factor eIF4E.
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Biophys J,
85,
1450-1456.
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N.Sonenberg,
and
T.E.Dever
(2003).
Eukaryotic translation initiation factors and regulators.
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Curr Opin Struct Biol,
13,
56-63.
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T.Preiss,
and
M.W Hentze
(2003).
Starting the protein synthesis machine: eukaryotic translation initiation.
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Bioessays,
25,
1201-1211.
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G.C.Scheper,
and
C.G.Proud
(2002).
Does phosphorylation of the cap-binding protein eIF4E play a role in translation initiation?
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Eur J Biochem,
269,
5350-5359.
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G.Calero,
K.F.Wilson,
T.Ly,
J.L.Rios-Steiner,
J.C.Clardy,
and
R.A.Cerione
(2002).
Structural basis of m7GpppG binding to the nuclear cap-binding protein complex.
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Nat Struct Biol,
9,
912-917.
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PDB codes:
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S.J.Morley,
and
S.Naegele
(2002).
Phosphorylation of eukaryotic initiation factor (eIF) 4E is not required for de novo protein synthesis following recovery from hypertonic stress in human kidney cells.
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J Biol Chem,
277,
32855-32859.
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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
codes are
shown on the right.
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Links
