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PDBsum entry 1fht
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Ribonucleoprotein
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PDB id
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1fht
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Contents |
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* Residue conservation analysis
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DOI no:
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J Mol Biol
257:398-411
(1996)
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PubMed id:
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Solution structure of the N-terminal RNP domain of U1A protein: the role of C-terminal residues in structure stability and RNA binding.
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J.M.Avis,
F.H.Allain,
P.W.Howe,
G.Varani,
K.Nagai,
D.Neuhaus.
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ABSTRACT
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The solution structure of a fragment of the human U1A spliceosomal protein
containing residues 2 to 117 (U1A117) determined using multi-dimensional
heteronuclear NMR is presented. The C-terminal region of the molecule is
considerably more ordered in the free protein than thought previously and its
conformation is different from that seen in the crystal structure of the complex
with U1 RNA hairpin II. The residues between Asp90 and Lys98 form an alpha-helix
that lies across the beta-sheet, with residues IIe93, IIe94 and Met97 making
contacts with Leu44, Phe56 and IIe58. This interaction prevents solvent exposure
of hydrophobic residues on the surface of the beta-sheet, thereby stabilising
the protein. Upon RNA binding, helix C moves away from this position, changing
its orientation by 135 degrees to allow Tyr13, Phe56 and Gln54 to stack with
bases of the RNA, and also allowing Leu44 to contact the RNA. The new position
of helix C in the complex with RNA is stabilised by hydrophobic interactions
from IIe93 and IIe94 to IIe58, Leu 41, Val62 and His 10, as well as a hydrogen
bond between Ser91 and Thr11. The movement of helix C mainly involves changes in
the main-chain torsion angles of Thr89, Asp90 and Ser91, the helix thereby
acting as a "lid" over the RNA binding surface.
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Selected figure(s)
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Figure 2.
Figure 2. Diagonal plot of the NOE constraints used to
calculate the structure of U1A117, as a function of
sequence. Filled squares indicate one or more constraints
between backbone atoms, filled triangles indicate one or
more backbone to side-chain constraints, and open circles
indicate one or more side-chain to side-chain constraints.
Constraints defining the antiparallel b4-bl-b3-b2 sheet
structure are indicated.
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Figure 5.
Figure 5. Schematic representation of the U1A117
protein (shown only to residue 105), produced using the
program MOLSCRIPT (Kraulis, 1991). The lowest energy
structure from amongst the ensemble of 43 is shown.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1996,
257,
398-411)
copyright 1996.
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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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D.Anunciado,
A.Dhar,
M.Gruebele,
and
A.M.Baranger
(2011).
Multistep kinetics of the U1A-SL2 RNA complex dissociation.
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J Mol Biol,
408,
896-908.
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G.Weber,
S.Trowitzsch,
B.Kastner,
R.Lührmann,
and
M.C.Wahl
(2010).
Functional organization of the Sm core in the crystal structure of human U1 snRNP.
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EMBO J,
29,
4172-4184.
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PDB code:
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A.Eulalio,
F.Tritschler,
R.Büttner,
O.Weichenrieder,
E.Izaurralde,
and
V.Truffault
(2009).
The RRM domain in GW182 proteins contributes to miRNA-mediated gene silencing.
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Nucleic Acids Res,
37,
2974-2983.
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PDB code:
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C.Netter,
G.Weber,
H.Benecke,
and
M.C.Wahl
(2009).
Functional stabilization of an RNA recognition motif by a noncanonical N-terminal expansion.
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RNA,
15,
1305-1313.
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PDB code:
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Q.C.An,
and
G.Y.Liu
(2009).
Molecular cloning, sequence identification, and tissue expression profile analysis of three novel porcine genes: SDHB, SNRPA and CRYBB1.
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Mol Biol Rep,
36,
683-690.
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D.Anunciado,
M.Agumeh,
B.L.Kormos,
D.L.Beveridge,
J.L.Knee,
and
A.M.Baranger
(2008).
Characterization of the dynamics of an essential helix in the U1A protein by time-resolved fluorescence measurements.
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J Phys Chem B,
112,
6122-6130.
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T.Nagata,
S.Suzuki,
R.Endo,
M.Shirouzu,
T.Terada,
M.Inoue,
T.Kigawa,
N.Kobayashi,
P.Güntert,
A.Tanaka,
Y.Hayashizaki,
Y.Muto,
and
S.Yokoyama
(2008).
The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.
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Nucleic Acids Res,
36,
4754-4767.
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PDB code:
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Y.Chen,
J.Mandic,
and
G.Varani
(2008).
Cell-free selection of RNA-binding proteins using in vitro compartmentalization.
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Nucleic Acids Res,
36,
e128.
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B.L.Kormos,
A.M.Baranger,
and
D.L.Beveridge
(2007).
A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations.
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J Struct Biol,
157,
500-513.
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B.L.Kormos,
Y.Benitex,
A.M.Baranger,
and
D.L.Beveridge
(2007).
Affinity and specificity of protein U1A-RNA complex formation based on an additive component free energy model.
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J Mol Biol,
371,
1405-1419.
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M.G.Caprara,
P.Chatterjee,
A.Solem,
K.L.Brady-Passerini,
and
B.J.Kaspar
(2007).
An allosteric-feedback mechanism for protein-assisted group I intron splicing.
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RNA,
13,
211-222.
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C.Dominguez,
and
F.H.Allain
(2006).
NMR structure of the three quasi RNA recognition motifs (qRRMs) of human hnRNP F and interaction studies with Bcl-x G-tract RNA: a novel mode of RNA recognition.
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Nucleic Acids Res,
34,
3634-3645.
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PDB codes:
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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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M.J.Law,
M.E.Linde,
E.J.Chambers,
C.Oubridge,
P.S.Katsamba,
L.Nilsson,
I.S.Haworth,
and
I.A.Laird-Offringa
(2006).
The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA.
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Nucleic Acids Res,
34,
275-285.
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M.J.Schellenberg,
R.A.Edwards,
D.B.Ritchie,
O.A.Kent,
M.M.Golas,
H.Stark,
R.Lührmann,
J.N.Glover,
and
A.M.MacMillan
(2006).
Crystal structure of a core spliceosomal protein interface.
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Proc Natl Acad Sci U S A,
103,
1266-1271.
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PDB codes:
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N.Dobson,
G.Dantas,
D.Baker,
and
G.Varani
(2006).
High-resolution structural validation of the computational redesign of human U1A protein.
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Structure,
14,
847-856.
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PDB code:
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R.C.Wilson,
C.J.Bohlen,
M.P.Foster,
and
C.E.Bell
(2006).
Structure of Pfu Pop5, an archaeal RNase P protein.
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Proc Natl Acad Sci U S A,
103,
873-878.
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PDB code:
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S.C.Walker,
and
D.R.Engelke
(2006).
Ribonuclease P: the evolution of an ancient RNA enzyme.
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Crit Rev Biochem Mol Biol,
41,
77.
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C.Maris,
C.Dominguez,
and
F.H.Allain
(2005).
The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression.
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FEBS J,
272,
2118-2131.
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M.J.Law,
E.J.Chambers,
P.S.Katsamba,
I.S.Haworth,
and
I.A.Laird-Offringa
(2005).
Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction.
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Nucleic Acids Res,
33,
2917-2928.
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N.Dobson,
G.Dantas,
and
G.Varani
(2005).
1H, 13C and 15N resonance assignments of URNdesign, a computationally redesigned RRM protein.
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J Biomol NMR,
33,
135.
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S.A.Showalter,
and
K.B.Hall
(2005).
Correlated motions in the U1 snRNA stem/loop 2:U1A RBD1 complex.
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Biophys J,
89,
2046-2058.
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V.Calabro,
M.D.Daugherty,
and
A.D.Frankel
(2005).
A single intermolecular contact mediates intramolecular stabilization of both RNA and protein.
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Proc Natl Acad Sci U S A,
102,
6849-6854.
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PDB code:
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V.Cojocaru,
S.Nottrott,
R.Klement,
and
T.M.Jovin
(2005).
The snRNP 15.5K protein folds its cognate K-turn RNA: a combined theoretical and biochemical study.
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RNA,
11,
197-209.
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V.Guallar,
and
K.W.Borrelli
(2005).
A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding.
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Proc Natl Acad Sci U S A,
102,
3954-3959.
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M.T.McClain,
C.S.Lutz,
K.M.Kaufman,
O.Z.Faig,
T.F.Gross,
and
J.A.James
(2004).
Structural availability influences the capacity of autoantigenic epitopes to induce a widespread lupus-like autoimmune response.
|
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Proc Natl Acad Sci U S A,
101,
3551-3556.
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N.Leulliot,
S.Quevillon-Cheruel,
M.Graille,
H.van Tilbeurgh,
T.C.Leeper,
K.S.Godin,
T.E.Edwards,
S.T.Sigurdsson,
N.Rozenkrants,
R.J.Nagel,
M.Ares,
and
G.Varani
(2004).
A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III.
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EMBO J,
23,
2468-2477.
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PDB codes:
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P.J.Simpson,
T.P.Monie,
A.Szendröi,
N.Davydova,
J.K.Tyzack,
M.R.Conte,
C.M.Read,
P.D.Cary,
D.I.Svergun,
P.V.Konarev,
S.Curry,
and
S.Matthews
(2004).
Structure and RNA interactions of the N-terminal RRM domains of PTB.
|
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Structure,
12,
1631-1643.
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PDB codes:
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A.Jacks,
J.Babon,
G.Kelly,
I.Manolaridis,
P.D.Cary,
S.Curry,
and
M.R.Conte
(2003).
Structure of the C-terminal domain of human La protein reveals a novel RNA recognition motif coupled to a helical nuclear retention element.
|
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Structure,
11,
833-843.
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PDB code:
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C.Phillips,
and
S.Gunderson
(2003).
Sequences adjacent to the 5' splice site control U1A binding upstream of the IgM heavy chain secretory poly(A) site.
|
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J Biol Chem,
278,
22102-22111.
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G.C.Pérez-Alvarado,
M.Martínez-Yamout,
M.M.Allen,
R.Grosschedl,
H.J.Dyson,
and
P.E.Wright
(2003).
Structure of the nuclear factor ALY: insights into post-transcriptional regulatory and mRNA nuclear export processes.
|
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Biochemistry,
42,
7348-7357.
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PDB code:
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J.M.Pérez Cañadillas,
and
G.Varani
(2003).
Recognition of GU-rich polyadenylation regulatory elements by human CstF-64 protein.
|
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EMBO J,
22,
2821-2830.
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PDB code:
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P.B.Rupert,
H.Xiao,
and
A.R.Ferré-D'Amaré
(2003).
U1A RNA-binding domain at 1.8 A resolution.
|
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Acta Crystallogr D Biol Crystallogr,
59,
1521-1524.
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PDB code:
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U.Kühn,
A.Nemeth,
S.Meyer,
and
E.Wahle
(2003).
The RNA binding domains of the nuclear poly(A)-binding protein.
|
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J Biol Chem,
278,
16916-16925.
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C.S.Lutz,
M.T.McClain,
J.B.Harley,
and
J.A.James
(2002).
Anti-U1A monoclonal antibodies recognize unique epitope targets of U1A which are involved in the binding of U1 RNA.
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J Mol Recognit,
15,
163-170.
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F.Pitici,
D.L.Beveridge,
and
A.M.Baranger
(2002).
Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: do molecular substates code for specificity?
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Biopolymers,
65,
424-435.
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I.D'Orso,
and
A.C.Frasch
(2002).
TcUBP-1, an mRNA destabilizing factor from trypanosomes, homodimerizes and interacts with novel AU-rich element- and Poly(A)-binding proteins forming a ribonucleoprotein complex.
|
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J Biol Chem,
277,
50520-50528.
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J.B.Tuite,
J.C.Shiels,
and
A.M.Baranger
(2002).
Substitution of an essential adenine in the U1A-RNA complex with a non-polar isostere.
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Nucleic Acids Res,
30,
5269-5275.
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J.C.Shiels,
J.B.Tuite,
S.J.Nolan,
and
A.M.Baranger
(2002).
Investigation of a conserved stacking interaction in target site recognition by the U1A protein.
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Nucleic Acids Res,
30,
550-558.
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P.S.Katsamba,
M.Bayramyan,
I.S.Haworth,
D.G.Myszka,
and
I.A.Laird-Offringa
(2002).
Complex role of the beta 2-beta 3 loop in the interaction of U1A with U1 hairpin II RNA.
|
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J Biol Chem,
277,
33267-33274.
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S.Kumar,
and
R.Nussinov
(2002).
Relationship between ion pair geometries and electrostatic strengths in proteins.
|
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Biophys J,
83,
1595-1612.
|
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E.Jankowsky,
C.H.Gross,
S.Shuman,
and
A.M.Pyle
(2001).
Active disruption of an RNA-protein interaction by a DExH/D RNA helicase.
|
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Science,
291,
121-125.
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J.M.Pérez-Cañadillas,
and
G.Varani
(2001).
Recent advances in RNA-protein recognition.
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Curr Opin Struct Biol,
11,
53-58.
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S.Kumar,
and
R.Nussinov
(2001).
Fluctuations in ion pairs and their stabilities in proteins.
|
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Proteins,
43,
433-454.
|
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W.Wang,
O.Donini,
C.M.Reyes,
and
P.A.Kollman
(2001).
Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions.
|
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Annu Rev Biophys Biomol Struct,
30,
211-243.
|
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C.Clerte,
and
K.B.Hall
(2000).
Spatial orientation and dynamics of the U1A proteins in the U1A-UTR complex.
|
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Biochemistry,
39,
7320-7329.
|
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J.M.Klein Gunnewiek,
R.I.Hussein,
Y.van Aarssen,
D.Palacios,
R.de Jong,
W.J.van Venrooij,
and
S.I.Gunderson
(2000).
Fourteen residues of the U1 snRNP-specific U1A protein are required for homodimerization, cooperative RNA binding, and inhibition of polyadenylation.
|
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Mol Cell Biol,
20,
2209-2217.
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M.R.Conte,
T.Grüne,
J.Ghuman,
G.Kelly,
A.Ladas,
S.Matthews,
and
S.Curry
(2000).
Structure of tandem RNA recognition motifs from polypyrimidine tract binding protein reveals novel features of the RRM fold.
|
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EMBO J,
19,
3132-3141.
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PDB code:
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P.Nissen,
M.Kjeldgaard,
and
J.Nyborg
(2000).
Macromolecular mimicry.
|
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EMBO J,
19,
489-495.
|
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C.M.Reyes,
and
P.A.Kollman
(1999).
Molecular dynamics studies of U1A-RNA complexes.
|
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RNA,
5,
235-244.
|
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D.E.Otzen,
O.Kristensen,
M.Proctor,
and
M.Oliveberg
(1999).
Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots.
|
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Biochemistry,
38,
6499-6511.
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PDB code:
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E.Wahle,
and
U.Rüegsegger
(1999).
3'-End processing of pre-mRNA in eukaryotes.
|
| |
FEMS Microbiol Rev,
23,
277-295.
|
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E.Welin Henriksson,
M.Wahren-Herlenius,
I.Lundberg,
E.Mellquist,
and
I.Pettersson
(1999).
Key residues revealed in a major conformational epitope of the U1-70K protein.
|
| |
Proc Natl Acad Sci U S A,
96,
14487-14492.
|
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J.M.Jean,
C.Clerte,
and
K.B.Hall
(1999).
Global and local dynamics of the human U1A protein determined by tryptophan fluorescence.
|
| |
Protein Sci,
8,
2110-2120.
|
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P.Hanachi,
J.W.Hershey,
and
H.P.Vornlocher
(1999).
Characterization of the p33 subunit of eukaryotic translation initiation factor-3 from Saccharomyces cerevisiae.
|
| |
J Biol Chem,
274,
8546-8553.
|
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T.Ternström,
U.Mayor,
M.Akke,
and
M.Oliveberg
(1999).
From snapshot to movie: phi analysis of protein folding transition states taken one step further.
|
| |
Proc Natl Acad Sci U S A,
96,
14854-14859.
|
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V.Gopalan,
H.Kühne,
R.Biswas,
H.Li,
G.W.Brudvig,
and
S.Altman
(1999).
Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using electron paramagnetic resonance spectroscopy.
|
| |
Biochemistry,
38,
1705-1714.
|
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|
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Y.Tang,
and
L.Nilsson
(1999).
Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution.
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Biophys J,
77,
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A.M.Edwards,
A.Bochkarev,
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Origin DNA-binding proteins.
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Curr Opin Struct Biol,
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B.Wang,
D.N.Jones,
B.P.Kaine,
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(1998).
High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases.
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| |
Structure,
6,
555-569.
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PDB code:
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D.L.Beck,
W.T.Stump,
and
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Defining the orientation of the human U1A RBD1 on its UTR by tethered-EDTA(Fe) cleavage.
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RNA,
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G.Varani,
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RNA recognition by RNP proteins during RNA processing.
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Annu Rev Biophys Biomol Struct,
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W.M.Clemons,
C.Davies,
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(1998).
Conformational variability of the N-terminal helix in the structure of ribosomal protein S15.
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| |
Structure,
6,
429-438.
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PDB code:
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A.Ramos,
C.C.Gubser,
and
G.Varani
(1997).
Recent solution structures of RNA and its complexes with drugs, peptides and proteins.
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A.Ramos,
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Structure of the acceptor stem of Escherichia coli tRNA Ala: role of the G3.U70 base pair in synthetase recognition.
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| |
Nucleic Acids Res,
25,
2083-2090.
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PDB code:
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F.H.Allain,
P.W.Howe,
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and
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(1997).
Structural basis of the RNA-binding specificity of human U1A protein.
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EMBO J,
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PDB code:
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G.Serin,
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L.Ghisolfi,
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Two RNA-binding domains determine the RNA-binding specificity of nucleolin.
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J.Lu,
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Tertiary structure of RBD2 and backbone dynamics of RBD1 and RBD2 of the human U1A protein determined by NMR spectroscopy.
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| |
Biochemistry,
36,
10393-10405.
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PDB code:
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J.Lu,
and
K.B.Hall
(1997).
Thermal unfolding of the N-terminal RNA binding domain of the human U1A protein studied by differential scanning calorimetry.
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Biophys Chem,
64,
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P.A.Bullock
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The initiation of simian virus 40 DNA replication in vitro.
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Crystal structure of the two RNA binding domains of human hnRNP A1 at 1.75 A resolution.
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| |
Nat Struct Biol,
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PDB code:
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F.Aboul-ela,
J.Karn,
and
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(1996).
Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge.
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| |
Nucleic Acids Res,
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PDB code:
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K.Nagai
(1996).
RNA-protein complexes.
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| |
Curr Opin Struct Biol,
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J.M.Avis,
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(1996).
Two structurally different RNA molecules are bound by the spliceosomal protein U1A using the same recognition strategy.
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| |
Structure,
4,
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PDB code:
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X.Luo,
D.G.Sanford,
P.A.Bullock,
and
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(1996).
Solution structure of the origin DNA-binding domain of SV40 T-antigen.
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| |
Nat Struct Biol,
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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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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