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PDBsum entry 1d3b
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RNA binding protein
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PDB id
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1d3b
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Contents |
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(+ 0 more)
72 a.a.
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81 a.a.
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86 a.a.
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structures of two sm protein complexes and their implications for the assembly of the spliceosomal snrnps.
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Authors
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C.Kambach,
S.Walke,
R.Young,
J.M.Avis,
E.De la fortelle,
V.A.Raker,
R.Lührmann,
J.Li,
K.Nagai.
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Ref.
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Cell, 1999,
96,
375-387.
[DOI no: ]
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PubMed id
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Abstract
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The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs)
involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F,
and G) in common, which assemble around the Sm site present in four of the major
spliceosomal small nuclear RNAs (snRNAs). These proteins share a common sequence
motif in two segments, Sm1 and Sm2, separated by a short variable linker.
Crystal structures of two Sm protein complexes, D3B and D1D2, show that these
proteins have a common fold containing an N-terminal helix followed by a
strongly bent five-stranded antiparallel beta sheet, and the D1D2 and D3B dimers
superpose closely in their core regions, including the dimer interfaces. The
crystal structures suggest that the seven Sm proteins could form a closed ring
and the snRNAs may be bound in the positively charged central hole.
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Figure 2.
Figure 2. Ribbon Representations of the Crystal Structure of
the D and B Proteins(A) D[3] protein (front view) with the
hydrogen bonding network involving Tyr-62 and highly conserved
residues Glu-36, Asn-40, Arg-64, and Gly-65.(B) D[3] protein
(side view).(C) B protein (front view) including highly
conserved residues Asp-35, Asn-39, Arg-73, and Gly-74. Strands
are color coded as in [3]Figure 1. Figure produced with SETOR (
[12]).
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Figure 4.
Figure 4. The Interaction between the D and B Proteins within
the Heterodimer(A) Stereo view of the D[3]B dimeric complex.
D[3], orange; B, blue. The β 5 strand of the D[3] protein pairs
with the β 4 strand of the B protein, forming a continuous
antiparallel β sheet. The loops L2, L3, L4, and L5 are
extending in the same direction.(B) Ball-and-stick model (stereo
view) of the main dimer interface stabilized by the paired β
strands and hydrophobic clustering of Phe-27 (strand β 2) of
the B protein and Phe-70 of the D[3] protein. The hydrogen bond
between the Gly-65 of D3 and Arg-73 of B stabilizes the
conformation of loop L5.(C) A close-up stereo view of the D[3]
and B protein interface including the hydrophobic cluster
between residues on the β sheet outer surface of the B protein
and residues on helix A and strands β 1β 2, and β 5 of the
D[3] protein. Pro-6 of the D[3] protein makes close contact with
Ala-33, the highly conserved Asp-35 and Asn-39, and Ile-41 of
the B protein.(D) The intersubunit salt bridge between Glu-21
(D[3]) and Arg-65 (B) and a cluster of arginines showing
stacking of the guanidinium groups (Arg-69 of D[3] and Arg-25
and Arg-49 of B). The sigma A–weighted 2Fo − Fc map
indicates the high quality of the electron density. Figure
produced with SETOR ([[3]12]).
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The above figures are
reprinted
by permission from Cell Press:
Cell
(1999,
96,
375-387)
copyright 1999.
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Secondary reference #1
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Title
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Structure and assembly of the spliceosomal small nuclear ribonucleoprotein particles.
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Authors
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C.Kambach,
S.Walke,
K.Nagai.
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Ref.
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Curr Opin Struct Biol, 1999,
9,
222-230.
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PubMed id
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