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PDBsum entry 1nrt
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Amino-acid transport
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PDB id
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1nrt
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Theoretical model |
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PDB id:
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Amino-acid transport
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Title:
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Ape-site tRNA, theoretical model
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Structure:
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Transfer ribonucleic acid. Chain: a, b, c. Synonym: yeast,phe t-RNA
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Source:
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Saccharomyces cerevisiae. Yeast
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Authors:
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R.K.Agrawal,P.Penczek,R.Grassucci,Y.Li,A.Leith,K.H.Nierhaus, J.Frank
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Key ref:
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J.Frank
et al.
(1995).
A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome.
Nature,
376,
441-444.
PubMed id:
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Date:
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15-Dec-95
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Release date:
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01-Apr-97
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G-C-G-G-A-U-U-U-A-2MG-C-U-C-A-G-H2U-H2U-G-G-G-A-G-A-G-C-M2G-C-C-A-G-A-OMC-U
...
76 bases
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G-C-G-G-A-U-U-U-A-2MG-C-U-C-A-G-H2U-H2U-G-G-G-A-G-A-G-C-M2G-C-C-A-G-A-OMC-U
...
76 bases
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G-C-G-G-A-U-U-U-A-2MG-C-U-C-A-G-H2U-H2U-G-G-G-A-G-A-G-C-M2G-C-C-A-G-A-OMC-U
...
76 bases
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Nature
376:441-444
(1995)
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PubMed id:
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A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome.
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J.Frank,
J.Zhu,
P.Penczek,
Y.Li,
S.Srivastava,
A.Verschoor,
M.Radermacher,
R.Grassucci,
R.K.Lata,
R.K.Agrawal.
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ABSTRACT
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The ribosome is formed by assembly of proteins and nucleic acids, and
synthesizes proteins according to genetic instructions in all organisms. Many of
the biochemical steps of this fundamental process are known, but a detailed
understanding requires a well-defined structural model of the ribosome. Electron
microscopy combined with image reconstruction of two-dimensional crystals or
single ribosomes has been the most promising technique, but the resolution of
the resulting models has been insufficient. Here we report a 25-A reconstruction
of the ribosome from Escherichia coli, obtained by combining 4,300 projections
of ice-embedded single particles. Our new reconstruction reveals a channel in
the small ribosomal subunit and a bifurcating tunnel in the large subunit which
may constitute pathways for the incoming message and the nascent polypeptide
chain, respectively. Based on these new findings, a three-dimensional model of
the basic framework of protein synthesis is presented.
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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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M.Valle
(2011).
Almost lost in translation. Cryo-EM of a dynamic macromolecular complex: the ribosome.
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Eur Biophys J,
40,
589-597.
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C.A.Milbury,
J.C.Lee,
J.J.Cannone,
P.M.Gaffney,
and
R.R.Gutell
(2010).
Fragmentation of the large subunit ribosomal RNA gene in oyster mitochondrial genomes.
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BMC Genomics,
11,
485.
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J.Frank,
and
R.L.Gonzalez
(2010).
Structure and dynamics of a processive Brownian motor: the translating ribosome.
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Annu Rev Biochem,
79,
381-412.
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S.Bhushan,
M.Gartmann,
M.Halic,
J.P.Armache,
A.Jarasch,
T.Mielke,
O.Berninghausen,
D.N.Wilson,
and
R.Beckmann
(2010).
alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel.
|
| |
Nat Struct Mol Biol,
17,
313-317.
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A.Yonath
(2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
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J R Soc Interface,
6,
S575-S585.
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C.W.Carter
(2009).
E pluribus tres: the 2009 nobel prize in chemistry.
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Structure,
17,
1558-1561.
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|
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G.Y.Soung,
J.L.Miller,
H.Koc,
and
E.C.Koc
(2009).
Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes.
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J Proteome Res,
8,
3390-3402.
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J.Frank
(2009).
Single-particle reconstruction of biological macromolecules in electron microscopy--30 years.
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Q Rev Biophys,
42,
139-158.
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J.R.Williamson,
V.Ramakrishnan,
T.Steitz,
and
A.Yonath
(2009).
The ribosome at atomic resolution.
|
| |
Cell,
139,
1041-1043.
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P.B.Moore
(2009).
The ribosome returned.
|
| |
J Biol,
8,
8.
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S.Chiba,
A.Lamsa,
and
K.Pogliano
(2009).
A ribosome-nascent chain sensor of membrane protein biogenesis in Bacillus subtilis.
|
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EMBO J,
28,
3461-3475.
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A.V.Pisarev,
V.G.Kolupaeva,
M.M.Yusupov,
C.U.Hellen,
and
T.V.Pestova
(2008).
Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes.
|
| |
EMBO J,
27,
1609-1621.
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E.Angov,
C.J.Hillier,
R.L.Kincaid,
and
J.A.Lyon
(2008).
Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host.
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PLoS ONE,
3,
e2189.
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J.E.Brock,
S.Pourshahian,
J.Giliberti,
P.A.Limbach,
and
G.R.Janssen
(2008).
Ribosomes bind leaderless mRNA in Escherichia coli through recognition of their 5'-terminal AUG.
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RNA,
14,
2159-2169.
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C.S.Fraser,
and
J.A.Doudna
(2007).
Quantitative studies of ribosome conformational dynamics.
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Q Rev Biophys,
40,
163-189.
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J.Frank,
H.Gao,
J.Sengupta,
N.Gao,
and
D.J.Taylor
(2007).
The process of mRNA-tRNA translocation.
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Proc Natl Acad Sci U S A,
104,
19671-19678.
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J.S.Weinger,
and
S.A.Strobel
(2007).
Exploring the mechanism of protein synthesis with modified substrates and novel intermediate mimics.
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Blood Cells Mol Dis,
38,
110-116.
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K.Mossman,
and
J.Frank
(2007).
Profile of Joachim Frank.
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Proc Natl Acad Sci U S A,
104,
19668-19670.
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L.A.Passmore,
T.M.Schmeing,
D.Maag,
D.J.Applefield,
M.G.Acker,
M.A.Algire,
J.R.Lorsch,
and
V.Ramakrishnan
(2007).
The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome.
|
| |
Mol Cell,
26,
41-50.
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M.O'connor
(2007).
Interaction between the ribosomal subunits: 16S rRNA suppressors of the lethal DeltaA1916 mutation in the 23S rRNA of Escherichia coli.
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Mol Genet Genomics,
278,
307-315.
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A.Liiv,
and
M.O'Connor
(2006).
Mutations in the intersubunit bridge regions of 23 S rRNA.
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J Biol Chem,
281,
29850-29862.
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A.S.Mankin
(2006).
Nascent peptide in the "birth canal" of the ribosome.
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Trends Biochem Sci,
31,
11-13.
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H.Stark,
and
R.Lührmann
(2006).
Cryo-electron microscopy of spliceosomal components.
|
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Annu Rev Biophys Biomol Struct,
35,
435-457.
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K.Mitra,
and
J.Frank
(2006).
Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps.
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Annu Rev Biophys Biomol Struct,
35,
299-317.
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B.S.Laursen,
H.P.Sørensen,
K.K.Mortensen,
and
H.U.Sperling-Petersen
(2005).
Initiation of protein synthesis in bacteria.
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Microbiol Mol Biol Rev,
69,
101-123.
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D.N.Wilson,
and
K.H.Nierhaus
(2005).
Ribosomal proteins in the spotlight.
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Crit Rev Biochem Mol Biol,
40,
243-267.
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S.Takyar,
R.P.Hickerson,
and
H.F.Noller
(2005).
mRNA helicase activity of the ribosome.
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Cell,
120,
49-58.
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A.Yonath,
and
A.Bashan
(2004).
Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics.
|
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Annu Rev Microbiol,
58,
233-251.
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C.M.Spahn,
E.Jan,
A.Mulder,
R.A.Grassucci,
P.Sarnow,
and
J.Frank
(2004).
Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
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Cell,
118,
465-475.
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W.P.Tate,
and
E.S.Poole
(2004).
The ribosome: lifting the veil from a fascinating organelle.
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Bioessays,
26,
582-588.
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A.R.Cukras,
D.R.Southworth,
J.L.Brunelle,
G.M.Culver,
and
R.Green
(2003).
Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex.
|
| |
Mol Cell,
12,
321-328.
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H.Gao,
J.Sengupta,
M.Valle,
A.Korostelev,
N.Eswar,
S.M.Stagg,
P.Van Roey,
R.K.Agrawal,
S.C.Harvey,
A.Sali,
M.S.Chapman,
and
J.Frank
(2003).
Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
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Cell,
113,
789-801.
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PDB codes:
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J.Frank
(2003).
Toward an understanding of the structural basis of translation.
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Genome Biol,
4,
237.
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J.Frank
(2003).
Electron microscopy of functional ribosome complexes.
|
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Biopolymers,
68,
223-233.
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M.R.Sharma,
E.C.Koc,
P.P.Datta,
T.M.Booth,
L.L.Spremulli,
and
R.K.Agrawal
(2003).
Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins.
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| |
Cell,
115,
97.
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P.B.Moore,
and
T.A.Steitz
(2003).
The structural basis of large ribosomal subunit function.
|
| |
Annu Rev Biochem,
72,
813-850.
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|
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T.A.Steitz,
and
P.B.Moore
(2003).
RNA, the first macromolecular catalyst: the ribosome is a ribozyme.
|
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Trends Biochem Sci,
28,
411-418.
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A.Abbott
(2002).
The society of proteins.
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Nature,
417,
894-896.
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I.D.Campbell
(2002).
Timeline: the march of structural biology.
|
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Nat Rev Mol Cell Biol,
3,
377-381.
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J.Frank
(2002).
Single-particle imaging of macromolecules by cryo-electron microscopy.
|
| |
Annu Rev Biophys Biomol Struct,
31,
303-319.
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P.B.Moore,
and
T.A.Steitz
(2002).
The involvement of RNA in ribosome function.
|
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Nature,
418,
229-235.
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A.Bashan,
I.Agmon,
R.Zarivach,
F.Schluenzen,
J.Harms,
M.Pioletti,
H.Bartels,
M.Gluehmann,
H.Hansen,
T.Auerbach,
F.Franceschi,
and
A.Yonath
(2001).
High-resolution structures of ribosomal subunits: initiation, inhibition, and conformational variability.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
43-56.
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C.H.Kiang
(2001).
Single-particle study of protein assembly.
|
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Phys Rev E Stat Nonlin Soft Matter Phys,
64,
041911.
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C.M.Spahn,
J.S.Kieft,
R.A.Grassucci,
P.A.Penczek,
K.Zhou,
J.A.Doudna,
and
J.Frank
(2001).
Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit.
|
| |
Science,
291,
1959-1962.
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C.M.Spahn,
R.Beckmann,
N.Eswar,
P.A.Penczek,
A.Sali,
G.Blobel,
and
J.Frank
(2001).
Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
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Cell,
107,
373-386.
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PDB codes:
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D.E.Brodersen,
A.P.Carter,
W.M.Clemons,
R.J.Morgan-Warren,
F.V.Murphy,
J.M.Ogle,
M.J.Tarry,
B.T.Wimberly,
and
V.Ramakrishnan
(2001).
Atomic structures of the 30S subunit and its complexes with ligands and antibiotics.
|
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Cold Spring Harb Symp Quant Biol,
66,
17-32.
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G.Z.Yusupova,
M.M.Yusupov,
J.H.Cate,
and
H.F.Noller
(2001).
The path of messenger RNA through the ribosome.
|
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Cell,
106,
233-241.
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PDB codes:
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I.S.Gabashvili,
S.T.Gregory,
M.Valle,
R.Grassucci,
M.Worbs,
M.C.Wahl,
A.E.Dahlberg,
and
J.Frank
(2001).
The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22.
|
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Mol Cell,
8,
181-188.
|
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|
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J.Frank
(2001).
Cryo-electron microscopy as an investigative tool: the ribosome as an example.
|
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Bioessays,
23,
725-732.
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J.Frank,
and
R.K.Agrawal
(2001).
Ratchet-like movements between the two ribosomal subunits: their implications in elongation factor recognition and tRNA translocation.
|
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Cold Spring Harb Symp Quant Biol,
66,
67-75.
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P.B.Moore
(2001).
The ribosome at atomic resolution.
|
| |
Biochemistry,
40,
3243-3250.
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R.Beckmann,
C.M.Spahn,
J.Frank,
and
G.Blobel
(2001).
The active 80S ribosome-Sec61 complex.
|
| |
Cold Spring Harb Symp Quant Biol,
66,
543-554.
|
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|
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R.Beckmann,
C.M.Spahn,
N.Eswar,
J.Helmers,
P.A.Penczek,
A.Sali,
J.Frank,
and
G.Blobel
(2001).
Architecture of the protein-conducting channel associated with the translating 80S ribosome.
|
| |
Cell,
107,
361-372.
|
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|
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R.Willumeit,
G.Diedrich,
S.Forthmann,
J.Beckmann,
R.P.May,
H.B.Stuhrmann,
and
K.H.Nierhaus
(2001).
Mapping proteins of the 50S subunit from Escherichia coli ribosomes.
|
| |
Biochim Biophys Acta,
1520,
7.
|
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|
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V.Ramakrishnan,
and
P.B.Moore
(2001).
Atomic structures at last: the ribosome in 2000.
|
| |
Curr Opin Struct Biol,
11,
144-154.
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C.Davies,
and
S.W.White
(2000).
Electrons and X-rays gang up on the ribosome.
|
| |
Structure,
8,
R41-R45.
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C.M.Spahn,
P.A.Penczek,
A.Leith,
and
J.Frank
(2000).
A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome.
|
| |
Structure,
8,
937-948.
|
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D.I.Juzumiene,
and
P.Wollenzien
(2000).
Organization of the 16S rRNA around its 5' terminus determined by photochemical crosslinking in the 30S ribosomal subunit.
|
| |
RNA,
6,
26-40.
|
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D.I.Svergun,
and
K.H.Nierhaus
(2000).
A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome.
|
| |
J Biol Chem,
275,
14432-14439.
|
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I.S.Gabashvili,
R.K.Agrawal,
C.M.Spahn,
R.A.Grassucci,
D.I.Svergun,
J.Frank,
and
P.Penczek
(2000).
Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
|
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Cell,
100,
537-549.
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PDB code:
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M.G.Gomez-Lorenzo,
C.M.Spahn,
R.K.Agrawal,
R.A.Grassucci,
P.Penczek,
K.Chakraburtty,
J.P.Ballesta,
J.L.Lavandera,
J.F.Garcia-Bustos,
and
J.Frank
(2000).
Three-dimensional cryo-electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17.5 A resolution.
|
| |
EMBO J,
19,
2710-2718.
|
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N.Polacek,
S.Patzke,
K.H.Nierhaus,
and
A.Barta
(2000).
Periodic conformational changes in rRNA: monitoring the dynamics of translating ribosomes.
|
| |
Mol Cell,
6,
159-171.
|
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P.Nissen,
J.Hansen,
N.Ban,
P.B.Moore,
and
T.A.Steitz
(2000).
The structural basis of ribosome activity in peptide bond synthesis.
|
| |
Science,
289,
920-930.
|
|
|
PDB codes:
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P.Nissen,
M.Kjeldgaard,
and
J.Nyborg
(2000).
Macromolecular mimicry.
|
| |
EMBO J,
19,
489-495.
|
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R.Brimacombe
(2000).
The bacterial ribosome at atomic resolution.
|
| |
Structure,
8,
R195-R200.
|
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|
|
R.K.Agrawal,
C.M.Spahn,
P.Penczek,
R.A.Grassucci,
K.H.Nierhaus,
and
J.Frank
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Identification of ribosome-ligand interactions using cleavage reagents.
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W.Liu,
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(1995).
Estimation of variance distribution in three-dimensional reconstruction. I. Theory.
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