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PDBsum entry 1sjq

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protein links
RNA binding protein PDB id
1sjq
Jmol
Contents
Protein chain
88 a.a. *
* Residue conservation analysis
PDB id:
1sjq
Name: RNA binding protein
Title: Nmr structure of rrm1 from human polypyrimidine tract binding protein isoform 1 (ptb1)
Structure: Polypyrimidine tract-binding protein 1. Chain: a. Fragment: rrm1, residues 54-147. Synonym: ptb, heterogeneous nuclear ribonucleoprotein i, hnrnp i, 57 kda RNA-binding protein pptb-1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ptbp1, ptb. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 16 models
Authors: P.J.Simpson,T.P.Monie,A.Szendroi,N.Davydova,J.K.Tyzack, M.R.Conte,C.M.Read,P.D.Cary,D.I.Svergun,P.V.Konarev, M.V.Petoukhov,S.Curry,S.J.Matthews
Key ref:
P.J.Simpson et al. (2004). Structure and RNA interactions of the N-terminal RRM domains of PTB. Structure, 12, 1631-1643. PubMed id: 15341728 DOI: 10.1016/j.str.2004.07.008
Date:
04-Mar-04     Release date:   14-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26599  (PTBP1_HUMAN) -  Polypyrimidine tract-binding protein 1
Seq:
Struc:
 
Seq:
Struc:
531 a.a.
88 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

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

 

 
DOI no: 10.1016/j.str.2004.07.008 Structure 12:1631-1643 (2004)
PubMed id: 15341728  
 
 
Structure and RNA interactions of the N-terminal RRM domains of PTB.
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, S.Matthews.
 
  ABSTRACT  
 
The polypyrimidine tract binding protein (PTB) is an important regulator of alternative splicing that also affects mRNA localization, stabilization, polyadenylation, and translation. NMR structural analysis of the N-terminal half of PTB (residues 55-301) shows a canonical structure for RRM1 but reveals novel extensions to the beta strands and C terminus of RRM2 that significantly modify the beta sheet RNA binding surface. Although PTB contains four RNA recognition motifs (RRMs), it is widely held that only RRMs 3 and 4 are involved in RNA binding and that RRM2 mediates homodimerization. However, we show here not only that the RRMs 1 and 2 contribute substantially to RNA binding but also that full-length PTB is monomeric, with an elongated structure determined by X-ray solution scattering that is consistent with a linear arrangement of the constituent RRMs. These new insights into the structure and RNA binding properties of PTB suggest revised models of its mechanism of action.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. PTB Constructs Used in This StudyRRM domains are shaded gray. Construct boundaries are indicated by dashed lines; a dotted line indicates the N terminus resulting from proteolytic cleavage of PTB1-2.
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1631-1643) copyright 2004.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21241883 C.Dominguez, M.Schubert, O.Duss, S.Ravindranathan, and F.H.Allain (2011).
Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy.
  Prog Nucl Magn Reson Spectrosc, 58, 1.  
20080103 C.M.Maynard, and K.B.Hall (2010).
Interactions between PTB RRMs induce slow motions and increase RNA binding affinity.
  J Mol Biol, 397, 260-277.  
20859255 P.Kafasla, N.Morgner, C.V.Robinson, and R.J.Jackson (2010).
Polypyrimidine tract-binding protein stimulates the poliovirus IRES by modulating eIF4G binding.
  EMBO J, 29, 3710-3722.  
20795951 S.P.Han, Y.H.Tang, and R.Smith (2010).
Functional diversity of the hnRNPs: past, present and perspectives.
  Biochem J, 430, 379-392.  
20507978 T.R.Sweeney, V.Cisnetto, D.Bose, M.Bailey, J.R.Wilson, X.Zhang, G.J.Belsham, and S.Curry (2010).
Foot-and-mouth disease virus 2C is a hexameric AAA+ protein with a coordinated ATP hydrolysis mechanism.
  J Biol Chem, 285, 24347-24359.  
19226116 C.Clerte, and K.B.Hall (2009).
The domains of polypyrimidine tract binding protein have distinct RNA structural preferences.
  Biochemistry, 48, 2063-2074.  
19861426 D.C.Reid, B.L.Chang, S.I.Gunderson, L.Alpert, W.A.Thompson, and W.G.Fairbrother (2009).
Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence.
  RNA, 15, 2385-2397.  
19197356 J.Yang, C.Y.Chan, B.Jiang, X.Yu, G.Z.Zhu, Y.Chen, J.Barnard, and W.Mei (2009).
hnRNP I Inhibits Notch Signaling and Regulates Intestinal Epithelial Homeostasis in the Zebrafish.
  PLoS Genet, 5, e1000363.  
19583805 K.Masuda, K.Abdelmohsen, and M.Gorospe (2009).
RNA-binding proteins implicated in the hypoxic response.
  J Cell Mol Med, 13, 2759-2769.  
19740508 V.Fontanes, S.Raychaudhuri, and A.Dasgupta (2009).
A cell-permeable peptide inhibits hepatitis C virus replication by sequestering IRES transacting factors.
  Virology, 394, 82-90.  
18205209 C.Hidalgo-Curtis, A.Chase, M.Drachenberg, M.W.Roberts, J.Z.Finkelstein, S.Mould, D.Oscier, N.C.Cross, and F.H.Grand (2008).
The t(1;9)(p34;q34) and t(8;12)(p11;q15) fuse pre-mRNA processing proteins SFPQ (PSF) and CPSF6 to ABL and FGFR1.
  Genes Chromosomes Cancer, 47, 379-385.  
18842594 J.L.Jenkins, H.Shen, M.R.Green, and C.L.Kielkopf (2008).
Solution Conformation and Thermodynamic Characteristics of RNA Binding by the Splicing Factor U2AF65.
  J Biol Chem, 283, 33641-33649.  
19100700 Z.Wu, X.Jia, L.de la Cruz, X.C.Su, B.Marzolf, P.Troisch, D.Zak, A.Hamilton, B.Whittle, D.Yu, D.Sheahan, E.Bertram, A.Aderem, G.Otting, C.C.Goodnow, and G.F.Hoyne (2008).
Memory T cell RNA rearrangement programmed by heterogeneous nuclear ribonucleoprotein hnRNPLL.
  Immunity, 29, 863-875.  
17592047 A.J.Matlin, J.Southby, C.Gooding, and C.W.Smith (2007).
Repression of alpha-actinin SM exon splicing by assisted binding of PTB to the polypyrimidine tract.
  RNA, 13, 1214-1223.  
17548433 C.Paradis, P.Cloutier, L.Shkreta, J.Toutant, K.Klarskov, and B.Chabot (2007).
hnRNP I/PTB can antagonize the splicing repressor activity of SRp30c.
  RNA, 13, 1287-1300.  
17552919 M.Niepmann (2007).
Discontinuous native protein gel electrophoresis: pros and cons.
  Expert Rev Proteomics, 4, 355-361.  
17786225 S.D.Shaw, S.Chakrabarti, G.Ghosh, and A.R.Krainer (2007).
Deletion of the N-terminus of SF2/ASF permits RS-domain-independent pre-mRNA splicing.
  PLoS ONE, 2, e854.  
17690690 T.P.Monie, A.J.Perrin, J.R.Birtley, T.R.Sweeney, I.Karakasiliotis, Y.Chaudhry, L.O.Roberts, S.Matthews, I.G.Goodfellow, and S.Curry (2007).
Structural insights into the transcriptional and translational roles of Ebp1.
  EMBO J, 26, 3936-3944.
PDB code: 2v6c
16936729 A.P.Rideau, C.Gooding, P.J.Simpson, T.P.Monie, M.Lorenz, S.Hüttelmaier, R.H.Singer, S.Matthews, S.Curry, and C.W.Smith (2006).
A peptide motif in Raver1 mediates splicing repression by interaction with the PTB RRM2 domain.
  Nat Struct Mol Biol, 13, 839-848.  
16431980 C.Clerte, and K.B.Hall (2006).
Characterization of multimeric complexes formed by the human PTB1 protein on RNA.
  RNA, 12, 457-475.  
16818232 E.A.Sickmier, K.E.Frato, H.Shen, S.R.Paranawithana, M.R.Green, and C.L.Kielkopf (2006).
Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65.
  Mol Cell, 23, 49-59.
PDB codes: 2fzr 2g4b
16282332 F.Robinson, and C.W.Smith (2006).
A splicing repressor domain in polypyrimidine tract-binding protein.
  J Biol Chem, 281, 800-806.  
16362043 F.Vitali, A.Henning, F.C.Oberstrass, Y.Hargous, S.D.Auweter, M.Erat, and F.H.Allain (2006).
Structure of the two most C-terminal RNA recognition motifs of PTB using segmental isotope labeling.
  EMBO J, 25, 150-162.
PDB code: 2evz
16765895 M.V.Petoukhov, T.P.Monie, F.H.Allain, S.Matthews, S.Curry, and D.I.Svergun (2006).
Conformation of polypyrimidine tract binding protein in solution.
  Structure, 14, 1021-1027.  
16403634 R.Spellman, and C.W.Smith (2006).
Novel modes of splicing repression by PTB.
  Trends Biochem Sci, 31, 73-76.  
15840818 B.Amir-Ahmady, P.L.Boutz, V.Markovtsov, M.L.Phillips, and D.L.Black (2005).
Exon repression by polypyrimidine tract binding protein.
  RNA, 11, 699-716.  
15853797 C.Maris, C.Dominguez, and F.H.Allain (2005).
The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression.
  FEBS J, 272, 2118-2131.  
16179478 F.C.Oberstrass, S.D.Auweter, M.Erat, Y.Hargous, A.Henning, P.Wenter, L.Reymond, B.Amir-Ahmady, S.Pitsch, D.L.Black, and F.H.Allain (2005).
Structure of PTB bound to RNA: specific binding and implications for splicing regulation.
  Science, 309, 2054-2057.
PDB codes: 2ad9 2adb 2adc
15900315 K.A.Spriggs, M.Bushell, S.A.Mitchell, and A.E.Willis (2005).
Internal ribosome entry segment-mediated translation during apoptosis: the role of IRES-trans-acting factors.
  Cell Death Differ, 12, 585-591.  
15998809 S.A.Mitchell, K.A.Spriggs, M.Bushell, J.R.Evans, M.Stoneley, J.P.Le Quesne, R.V.Spriggs, and A.E.Willis (2005).
Identification of a motif that mediates polypyrimidine tract-binding protein-dependent internal ribosome entry.
  Genes Dev, 19, 1556-1571.  
16314454 T.P.Monie, H.Hernandez, C.V.Robinson, P.Simpson, S.Matthews, and S.Curry (2005).
The polypyrimidine tract binding protein is a monomer.
  RNA, 11, 1803-1808.  
16314455 Y.Song, E.Tzima, K.Ochs, G.Bassili, H.Trusheim, M.Linder, K.T.Preissner, and M.Niepmann (2005).
Evidence for an RNA chaperone function of polypyrimidine tract-binding protein in picornavirus translation.
  RNA, 11, 1809-1824.  
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 code is shown on the right.