PDBsum entry 2mst

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protein links
RNA binding protein PDB id
Protein chain
75 a.a. *
* Residue conservation analysis
PDB id:
Name: RNA binding protein
Title: Musashi1 rbd2, nmr
Structure: Protein (musashi1). Chain: a. Fragment: RNA-binding domain. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_cell: bl21(de3). Other_details: pcr
NMR struc: 20 models
Authors: T.Nagata,R.Kanno,Y.Kurihara,S.Uesugi,T.Imai,S.Sakakibara, H.Okano,M.Katahira
Key ref:
T.Nagata et al. (1999). Structure, backbone dynamics and interactions with RNA of the C-terminal RNA-binding domain of a mouse neural RNA-binding protein, Musashi1. J Mol Biol, 287, 315-330. PubMed id: 10080895 DOI: 10.1006/jmbi.1999.2596
19-May-99     Release date:   19-May-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q61474  (MSI1H_MOUSE) -  RNA-binding protein Musashi homolog 1
362 a.a.
75 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     2 terms  


DOI no: 10.1006/jmbi.1999.2596 J Mol Biol 287:315-330 (1999)
PubMed id: 10080895  
Structure, backbone dynamics and interactions with RNA of the C-terminal RNA-binding domain of a mouse neural RNA-binding protein, Musashi1.
T.Nagata, R.Kanno, Y.Kurihara, S.Uesugi, T.Imai, S.Sakakibara, H.Okano, M.Katahira.
Musashi1 is an RNA-binding protein abundantly expressed in the developing mouse central nervous system. Its restricted expression in neural precursor cells suggests that it is involved in the regulation of asymmetric cell division. Musashi1 contains two ribonucleoprotein (RNP)-type RNA-binding domains (RBDs), RBD1 and RBD2. Our previous studies showed that RBD1 alone binds to RNA, while the binding of RBD2 is not detected under the same conditions. Joining of RBD2 to RBD1, however, increases the affinity to greater than that of RBD1 alone, indicating that RBD2 contributes to RNA-binding. We have determined the three-dimensional solution structure of the C-terminal RBD (RBD2) of Musashi1 by NMR. It folds into a compact alpha beta structure comprising a four-stranded antiparallel beta-sheet packed against two alpha-helices, which is characteristic of RNP-type RBDs. Special structural features of RBD2 include a beta-bulge in beta2 and a shallow twist of the beta-sheet. The smaller 1H-15N nuclear Overhauser enhancement values for the residues of loop 3 between beta2 and beta3 suggest that this loop is flexible in the time-scale of nano- to picosecond order. The smaller 15N T2 values for the residues around the border between alpha2 and the following loop (loop 5) suggest this region undergoes conformational exchange in the milli- to microsecond time-scale. Chemical shift perturbation analysis indicated that RBD2 binds to an RNA oligomer obtained by in vitro selection under the conditions for NMR measurements, and thus the nature of the weak RNA-binding of RBD2 was successfully characterized by NMR, which is otherwise difficult to assess. Mainly the residues of the surface composed of the four-stranded beta-sheet, loops and C-terminal region are involved in the interaction. The appearance of side-chain NH proton resonances of arginine residues of loop 3 and imino proton resonances of RNA bases upon complex formation suggests the formation of intermolecular hydrogen bonds. The structural arrangement of the rings of the conserved aromatic residues of beta2 and beta3 is suitable for stacking interaction with RNA bases, known to be one of the major protein-RNA interactions, but a survey of the perturbation data suggested that the stacking interaction is not ideally achieved in the complex, which may be related to the weaker RNA-binding of RBD2.
  Selected figure(s)  
Figure 3.
Figure 3. The four-stranded antiparallel β-sheet of RBD2. Interstrand NOEs are indicated by double-headed continuous arrows, the NOEs with ambiguity due to overlapping being indicated by double-headed broken arrows. Slowly exchanging amide protons are indicated by bold H. Hydrogen bonds consistent with the NOEs and exchange data are indicated by broken lines. Black boxes on C^α indicate that the side-chains of these residues are presumed to point inside the protein.
Figure 4.
Figure 4. The structure of RBD2. (a) Superposition of the main-chains of 20 refined structures. N and C indicate K110 and A184, respectively, and loop 3 is labeled. (b) Schematic drawing of the restrained energy minimized mean structure derived from the 20 refined structures, as viewed from the same direction as that in (a). (c) Hydrophobic core. Overlaying of the 20 structures of the side-chains for residues involved in the hydrophobic core is shown on the main-chain of the restrained energy minimized mean structure. α-Helices and β-strands are colored red and sky-blue, respectively. (d) Hydrophobic patch exposed to the solvent. The same overlaying as that in (c) is shown for F112, F152 and F154, being rotated by ca 90 ° from that in (c).
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 287, 315-330) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
21320487 P.E.Nickerson, T.Myers, D.B.Clarke, and R.L.Chow (2011).
Changes in Musashi-1 subcellular localization correlate with cell cycle exit during postnatal retinal development.
  Exp Eye Res, 92, 344-352.  
20717979 T.Nagata, E.Niyada, N.Fujimoto, Y.Nagasaki, K.Noto, Y.Miyanoiri, J.Murata, K.Hiratsuka, and M.Katahira (2010).
Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1: mechanism for an increase in DNA-binding affinity through phosphorylation.
  Proteins, 78, 3033-3047.
PDB codes: 2ebi 2jmw
19657021 M.T.Liu, Y.H.Kuan, J.Wang, R.Hen, and M.D.Gershon (2009).
5-HT4 receptor-mediated neuroprotection and neurogenesis in the enteric nervous system of adult mice.
  J Neurosci, 29, 9683-9699.  
18641416 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.
  Nucleic Acids Res, 36, 4754-4767.
PDB code: 2rok
16106215 M.A.Lovell, and W.R.Markesbery (2005).
Ectopic expression of Musashi-1 in Alzheimer disease and Pick disease.
  J Neuropathol Exp Neurol, 64, 675-680.  
12907678 Y.Miyanoiri, H.Kobayashi, T.Imai, M.Watanabe, T.Nagata, S.Uesugi, H.Okano, and M.Katahira (2003).
Origin of higher affinity to RNA of the N-terminal RNA-binding domain than that of the C-terminal one of a mouse neural protein, musashi1, as revealed by comparison of their structures, modes of interaction, surface electrostatic potentials, and backbone dynamics.
  J Biol Chem, 278, 41309-41315.
PDB code: 1uaw
11222770 H.Izumi, T.Imamura, G.Nagatani, T.Ise, T.Murakami, H.Uramoto, T.Torigoe, H.Ishiguchi, Y.Yoshida, M.Nomoto, T.Okamoto, T.Uchiumi, M.Kuwano, K.Funa, and K.Kohno (2001).
Y box-binding protein-1 binds preferentially to single-stranded nucleic acids and exhibits 3'-->5' exonuclease activity.
  Nucleic Acids Res, 29, 1200-1207.  
11359897 T.Imai, A.Tokunaga, T.Yoshida, M.Hashimoto, K.Mikoshiba, G.Weinmaster, M.Nakafuku, and H.Okano (2001).
The neural RNA-binding protein Musashi1 translationally regulates mammalian numb gene expression by interacting with its mRNA.
  Mol Cell Biol, 21, 3888-3900.  
10745010 H.Pan, and D.B.Wigley (2000).
Structure of the zinc-binding domain of Bacillus stearothermophilus DNA primase.
  Structure, 8, 231-239.
PDB code: 1d0q
10856256 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.
  EMBO J, 19, 3132-3141.
PDB code: 1qm9
10830496 Y.Ishii, H.Yamada, T.Yamashino, K.Ohashi, E.Katoh, H.Shindo, T.Yamazaki, and T.Mizuno (2000).
Deletion of the yhhP gene results in filamentous cell morphology in Escherichia coli.
  Biosci Biotechnol Biochem, 64, 799-807.  
10449418 T.Ito, Y.Muto, M.R.Green, and S.Yokoyama (1999).
Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)).
  EMBO J, 18, 4523-4534.
PDB codes: 1u2f 2u2f
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.