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PDBsum entry 1qm9

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protein links
Ribonucleoprotein PDB id
1qm9
Jmol
Contents
Protein chain
198 a.a. *
* Residue conservation analysis
PDB id:
1qm9
Name: Ribonucleoprotein
Title: Nmr, representative structure
Structure: Polypyrimidine tract-binding protein. Chain: a. Fragment: RNA binding fragment. Synonym: ptb, ptb-c198, heterogeneous nuclear ribonucleoprotein i, hnrnp i, 57 kd RNA-binding protein pptb-1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: nucleus/cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 469008.
NMR struc: 1 models
Authors: M.R.Conte,T.Grune,S.Curry,S.Matthews
Key ref:
M.R.Conte et al. (2000). Structure of tandem RNA recognition motifs from polypyrimidine tract binding protein reveals novel features of the RRM fold. EMBO J, 19, 3132-3141. PubMed id: 10856256 DOI: 10.1093/emboj/19.12.3132
Date:
22-Sep-99     Release date:   03-Jul-00    
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.
198 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!
  Cellular component     nucleus   1 term 
  Biological process     mRNA processing   1 term 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1093/emboj/19.12.3132 EMBO J 19:3132-3141 (2000)
PubMed id: 10856256  
 
 
Structure of tandem RNA recognition motifs from polypyrimidine tract binding protein reveals novel features of the RRM fold.
M.R.Conte, T.Grüne, J.Ghuman, G.Kelly, A.Ladas, S.Matthews, S.Curry.
 
  ABSTRACT  
 
Polypyrimidine tract binding protein (PTB), an RNA binding protein containing four RNA recognition motifs (RRMs), is involved in both pre-mRNA splicing and translation initiation directed by picornaviral internal ribosome entry sites. Sequence comparisons previously indicated that PTB is a non-canonical RRM protein. The solution structure of a PTB fragment containing RRMs 3 and 4 shows that the protein consists of two domains connected by a long, flexible linker. The two domains tumble independently in solution, having no fixed relative orientation. In addition to the betaalphabetabetaalphabeta topology, which is characteristic of RRM domains, the C-terminal extension of PTB RRM-3 incorporates an unanticipated fifth beta-strand, which extends the RNA binding surface. The long, disordered polypeptide connecting beta4 and beta5 in RRM-3 is poised above the RNA binding surface and is likely to contribute to RNA recognition. Mutational analyses show that both RRM-3 and RRM-4 contribute to RNA binding specificity and that, despite its unusual sequence, PTB binds RNA in a manner akin to that of other RRM proteins.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Ribbon diagrams for PTB-34 and Sex-lethal. (A) Comparison of tandem domain structures of PTB and Sex-lethal. The relative orientation of the two domains shown for PTB is arbitrary, as is the structure of the inter-domain linker. The structure of Sex-lethal was solved crystallographically in the presence of bound RNA (Handa et al., 1999), which has been omitted from the figure. (B) Comparison of RRM-3 and RRM-4 domains from PTB with RRM-1 of Sex-lethal. PTB RRM-3 contains an additional strand ( 5) on one side of the RNA binding surface. Note that the conformation shown for the 4– 5 loop is only one of many conformations that are consistent with the data (see Figure 2).
Figure 5.
Figure 5 Overview of protein and RNA constructs used in this study. (A) Schematic depiction of PTB constructs; RRM domains are indicated by shading. (B) Schematic diagram of the EMCV IRES; domain 1 is boxed.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 3132-3141) copyright 2000.  
  Figures were 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.  
21423341 J.Suckale, O.Wendling, J.Masjkur, M.Jäger, C.Münster, K.Anastassiadis, A.F.Stewart, and M.Solimena (2011).
PTBP1 is required for embryonic development before gastrulation.
  PLoS One, 6, e16992.  
21292163 Y.Bai, S.K.Srivastava, J.H.Chang, J.L.Manley, and L.Tong (2011).
Structural basis for dimerization and activity of human PAPD1, a noncanonical poly(A) polymerase.
  Mol Cell, 41, 311-320.
PDB code: 3pq1
20150968 A.Pacheco, and E.Martinez-Salas (2010).
Insights into the biology of IRES elements through riboproteomic approaches.
  J Biomed Biotechnol, 2010, 458927.  
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.  
20336253 F.Liu, C.Maynard, G.Scott, A.Melnykov, K.B.Hall, and M.Gruebele (2010).
A natural missing link between activated and downhill protein folding scenarios.
  Phys Chem Chem Phys, 12, 3542-3549.  
19690964 L.Skrisovska, M.Schubert, and F.H.Allain (2010).
Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins.
  J Biomol NMR, 46, 51-65.  
19066202 A.Pacheco, S.López de Quinto, J.Ramajo, N.Fernández, and E.Martínez-Salas (2009).
A novel role for Gemin5 in mRNA translation.
  Nucleic Acids Res, 37, 582-590.  
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.  
19308324 K.Teilum, J.G.Olsen, and B.B.Kragelund (2009).
Functional aspects of protein flexibility.
  Cell Mol Life Sci, 66, 2231-2247.  
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.  
18059478 G.V.Crichlow, H.Zhou, H.H.Hsiao, K.B.Frederick, M.Debrosse, Y.Yang, E.J.Folta-Stogniew, H.J.Chung, C.Fan, E.M.De la Cruz, D.Levens, E.Lolis, and D.Braddock (2008).
Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition.
  EMBO J, 27, 277-289.
PDB code: 2qfj
17400915 N.Sari, Y.He, V.Doseeva, K.Surabian, J.Ramprakash, F.Schwarz, O.Herzberg, and J.Orban (2007).
Solution structure of HI1506, a novel two-domain protein from Haemophilus influenzae.
  Protein Sci, 16, 977-982.
PDB code: 2out
17850751 P.B.Balbo, and A.Bohm (2007).
Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis.
  Structure, 15, 1117-1131.
PDB code: 2q66
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
16973591 A.Nayak, I.G.Goodfellow, K.E.Woolaway, J.Birtley, S.Curry, and G.J.Belsham (2006).
Role of RNA structure and RNA binding activity of foot-and-mouth disease virus 3C protein in VPg uridylylation and virus replication.
  J Virol, 80, 9865-9875.  
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
16991206 M.Niepmann, and J.Zheng (2006).
Discontinuous native protein gel electrophoresis.
  Electrophoresis, 27, 3949-3951.  
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.  
16094695 S.Ilin, A.Hoskins, O.Ohlenschläger, H.R.Jonker, H.Schwalbe, and J.Wöhnert (2005).
Domain reorientation and induced fit upon RNA binding: solution structure and dynamics of ribosomal protein L11 from Thermotoga maritima.
  Chembiochem, 6, 1611-1618.
PDB code: 2k3f
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.  
16094605 V.N.Uversky, C.J.Oldfield, and A.K.Dunker (2005).
Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling.
  J Mol Recognit, 18, 343-384.  
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.  
14730023 H.Banerjee, A.Rahn, B.Gawande, S.Guth, J.Valcarcel, and R.Singh (2004).
The conserved RNA recognition motif 3 of U2 snRNA auxiliary factor (U2AF 65) is essential in vivo but dispensable for activity in vitro.
  RNA, 10, 240-253.  
15004547 J.Kadlec, E.Izaurralde, and S.Cusack (2004).
The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3.
  Nat Struct Mol Biol, 11, 330-337.
PDB code: 1uw4
14728692 L.S.Coles, M.A.Bartley, A.Bert, J.Hunter, S.Polyak, P.Diamond, M.A.Vadas, and G.J.Goodall (2004).
A multi-protein complex containing cold shock domain (Y-box) and polypyrimidine tract binding proteins forms on the vascular endothelial growth factor mRNA. Potential role in mRNA stabilization.
  Eur J Biochem, 271, 648-660.  
15341728 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.
  Structure, 12, 1631-1643.
PDB codes: 1sjq 1sjr
12842046 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.
  Structure, 11, 833-843.
PDB code: 1owx
12509450 B.J.Hamilton, A.Genin, R.Q.Cron, and W.F.Rigby (2003).
Delineation of a novel pathway that regulates CD154 (CD40 ligand) expression.
  Mol Cell Biol, 23, 510-525.  
12578833 C.Gooding, P.Kemp, and C.W.Smith (2003).
A novel polypyrimidine tract-binding protein paralog expressed in smooth muscle cells.
  J Biol Chem, 278, 15201-15207.  
12626338 D.L.Black (2003).
Mechanisms of alternative pre-messenger RNA splicing.
  Annu Rev Biochem, 72, 291-336.  
12704080 H.Shi, and R.M.Xu (2003).
Crystal structure of the Drosophila Mago nashi-Y14 complex.
  Genes Dev, 17, 971-976.
PDB code: 1oo0
14633994 N.Gromak, A.Rideau, J.Southby, A.D.Scadden, C.Gooding, S.Hüttelmaier, R.H.Singer, and C.W.Smith (2003).
The PTB interacting protein raver1 regulates alpha-tropomyosin alternative splicing.
  EMBO J, 22, 6356-6364.  
12191478 A.B.Hickman, D.R.Ronning, R.M.Kotin, and F.Dyda (2002).
Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep.
  Mol Cell, 10, 327-337.
PDB code: 1m55
12403469 A.Git, and N.Standart (2002).
The KH domains of Xenopus Vg1RBP mediate RNA binding and self-association.
  RNA, 8, 1319-1333.  
11911361 H.Liu, W.Zhang, R.B.Reed, W.Liu, and P.J.Grabowski (2002).
Mutations in RRM4 uncouple the splicing repression and RNA-binding activities of polypyrimidine tract binding protein.
  RNA, 8, 137-149.  
11917013 J.Vitali, J.Ding, J.Jiang, Y.Zhang, A.R.Krainer, and R.M.Xu (2002).
Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1.
  Nucleic Acids Res, 30, 1531-1538.
PDB code: 1l3k
11931771 N.Charlet-B, P.Logan, G.Singh, and T.A.Cooper (2002).
Dynamic antagonism between ETR-3 and PTB regulates cell type-specific alternative splicing.
  Mol Cell, 9, 649-658.  
12388766 P.Björk, G.Baurén, S.Jin, Y.G.Tong, T.R.Bürglin, U.Hellman, and L.Wieslander (2002).
A novel conserved RNA-binding domain protein, RBD-1, is essential for ribosome biogenesis.
  Mol Biol Cell, 13, 3683-3695.  
12004072 S.H.Back, S.Shin, and S.K.Jang (2002).
Polypyrimidine tract-binding proteins are cleaved by caspase-3 during apoptosis.
  J Biol Chem, 277, 27200-27209.  
11836431 S.H.Back, Y.K.Kim, W.J.Kim, S.Cho, H.R.Oh, J.E.Kim, and S.K.Jang (2002).
Translation of polioviral mRNA is inhibited by cleavage of polypyrimidine tract-binding proteins executed by polioviral 3C(pro).
  J Virol, 76, 2529-2542.  
11788707 X.Yuan, N.Davydova, M.R.Conte, S.Curry, and S.Matthews (2002).
Chemical shift mapping of RNA interactions with the polypyrimidine tract binding protein.
  Nucleic Acids Res, 30, 456-462.  
11179892 J.M.Pérez-Cañadillas, and G.Varani (2001).
Recent advances in RNA-protein recognition.
  Curr Opin Struct Biol, 11, 53-58.  
11421360 M.C.Wollerton, C.Gooding, F.Robinson, E.C.Brown, R.J.Jackson, and C.W.Smith (2001).
Differential alternative splicing activity of isoforms of polypyrimidine tract binding protein (PTB).
  RNA, 7, 819-832.  
11473790 P.J.Grabowski, and D.L.Black (2001).
Alternative RNA splicing in the nervous system.
  Prog Neurobiol, 65, 289-308.  
11134326 R.J.Maraia, and R.V.Intine (2001).
Recognition of nascent RNA by the human La antigen: conserved and divergent features of structure and function.
  Mol Cell Biol, 21, 367-379.  
  11739782 R.V.Kamath, D.J.Leary, and S.Huang (2001).
Nucleocytoplasmic shuttling of polypyrimidine tract-binding protein is uncoupled from RNA export.
  Mol Biol Cell, 12, 3808-3820.  
11724819 S.Hüttelmaier, S.Illenberger, I.Grosheva, M.Rüdiger, R.H.Singer, and B.M.Jockusch (2001).
Raver1, a dual compartment protein, is a ligand for PTB/hnRNPI and microfilament attachment proteins.
  J Cell Biol, 155, 775-786.  
11376140 X.Manival, L.Ghisolfi-Nieto, G.Joseph, P.Bouvet, and M.Erard (2001).
RNA-binding strategies common to cold-shock domain- and RNA recognition motif-containing proteins.
  Nucleic Acids Res, 29, 2223-2233.  
10958780 J.Bard, A.M.Zhelkovsky, S.Helmling, T.N.Earnest, C.L.Moore, and A.Bohm (2000).
Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP.
  Science, 289, 1346-1349.
PDB code: 1fa0
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.