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PDBsum entry 5gvq
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RNA binding protein
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PDB id
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5gvq
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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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Solution structure of the first rrm domain of human spliceosomal protein sf3b49
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Structure:
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Splicing factor 3b subunit 4. Chain: a. Synonym: spliceosomal protein sf3b49, pre-mRNA-splicing factor sf3b 49 kda subunit,spliceosome-associated protein 49,sap 49. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: sf3b4, sap49. Expressed in: escherichia coli. Expression_system_taxid: 562
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NMR struc:
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20 models
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Authors:
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K.Kuwasako,N.Nameki,K.Tsuda,M.Takahashi,A.Sato,N.Tochio,M.Inoue, T.Terada,T.Kigawa,N.Kobayashi,M.Shirouzu,T.Ito,T.Sakamoto, K.Wakamatsu,P.Guntert,S.Takahashi,S.Yokoyama,Y.Muto,Riken Structural Genomics/proteomics Initiative (Rsgi)
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Key ref:
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K.Kuwasako
et al.
(2017).
Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment.
Protein Sci,
26,
280-291.
PubMed id:
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Date:
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06-Sep-16
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Release date:
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12-Apr-17
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Supersedes:
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PROCHECK
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Headers
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References
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Q15427
(SF3B4_HUMAN) -
Splicing factor 3B subunit 4 from Homo sapiens
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Seq:
Struc:
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424 a.a.
105 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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*
PDB and UniProt seqs differ
at 10 residue positions (black
crosses)
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Protein Sci
26:280-291
(2017)
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PubMed id:
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Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment.
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K.Kuwasako,
N.Nameki,
K.Tsuda,
M.Takahashi,
A.Sato,
N.Tochio,
M.Inoue,
T.Terada,
T.Kigawa,
N.Kobayashi,
M.Shirouzu,
T.Ito,
T.Sakamoto,
K.Wakamatsu,
P.Güntert,
S.Takahashi,
S.Yokoyama,
Y.Muto.
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ABSTRACT
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The spliceosomal protein SF3b49, a component of the splicing factor 3b (SF3b)
protein complex in the U2 small nuclear ribonucleoprotein, contains two RNA
recognition motif (RRM) domains. In yeast, the first RRM domain (RRM1) of Hsh49
protein (yeast orthologue of human SF3b49) reportedly interacts with another
component, Cus1 protein (orthologue of human SF3b145). Here, we solved the
solution structure of the RRM1 of human SF3b49 and examined its mode of
interaction with a fragment of human SF3b145 using NMR methods. Chemical shift
mapping showed that the SF3b145 fragment spanning residues 598-631 interacts
with SF3b49 RRM1, which adopts a canonical RRM fold with a topology of
β1-α1-β2-β3-α2-β4. Furthermore, a docking model based on NOESY
measurements suggests that residues 607-616 of the SF3b145 fragment adopt a
helical structure that binds to RRM1 predominantly via α1, consequently
exhibiting a helix-helix interaction in almost antiparallel. This mode of
interaction was confirmed by a mutational analysis using GST pull-down assays.
Comparison with structures of all RRM domains when complexed with a peptide
found that this helix-helix interaction is unique to SF3b49 RRM1. Additionally,
all amino acid residues involved in the interaction are well conserved among
eukaryotes, suggesting evolutionary conservation of this interaction mode
between SF3b49 RRM1 and SF3b145.
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