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PDBsum entry 1dz5

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protein dna_rna Protein-protein interface(s) links
Ribonucleoprotein/RNA PDB id
1dz5
Jmol PyMol
Contents
Protein chain
101 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
1dz5
Name: Ribonucleoprotein/RNA
Title: The nmr structure of the 38kda u1a protein-pie RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human u1a protein
Structure: U1 small nuclear ribonucleoprotein a. Chain: a, b. Fragment: residues 2-102. Synonym: u1 snrnp a, u1-a, u1a. Engineered: yes. Mutation: yes. Pie, RNA (5'-r( Gp Ap Gp Ap Cp Ap Up Up Gp Cp Ap Cp Gp Gp Ap Gp Up Cp Up C)-3'). Chain: c, d.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 9606 other_details: produced by in vitro transcription.
NMR struc: 13 models
Authors: L.Varani,S.I.Gunderson,I.W.Mattaj,L.E.Kay,D.Neuhaus,G.Varani
Key ref:
L.Varani et al. (2000). The NMR structure of the 38 kDa U1A protein - PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein. Nat Struct Biol, 7, 329-335. PubMed id: 10742179 DOI: 10.1038/74101
Date:
16-Feb-00     Release date:   29-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P09012  (SNRPA_HUMAN) -  U1 small nuclear ribonucleoprotein A
Seq:
Struc:
282 a.a.
101 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     1 term  

 

 
DOI no: 10.1038/74101 Nat Struct Biol 7:329-335 (2000)
PubMed id: 10742179  
 
 
The NMR structure of the 38 kDa U1A protein - PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein.
L.Varani, S.I.Gunderson, I.W.Mattaj, L.E.Kay, D.Neuhaus, G.Varani.
 
  ABSTRACT  
 
The status of the poly(A) tail at the 3'-end of mRNAs controls the expression of numerous genes in response to developmental and extracellular signals. Poly(A) tail regulation requires cooperative binding of two human U1A proteins to an RNA regulatory region called the polyadenylation inhibition element (PIE). When bound to PIE RNA, U1A proteins also bind to the enzyme responsible for formation of the mature 3'-end of most eukaryotic mRNAs, poly(A) polymerase (PAP). The NMR structure of the 38 kDa complex formed between two U1A molecules and PIE RNA shows that binding cooperativity depends on helix C located at the end of the RNA-binding domain and just adjacent to the PAP-interacting domain of U1A. Since helix C undergoes a conformational change upon RNA binding, the structure shows that binding cooperativity and interactions with PAP occur only when U1A is bound to its cognate RNA. This mechanism ensures that the activity of PAP enzyme, which is essential to the cell, is only down regulated when U1A is bound to the U1A mRNA.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Structure of the trimolecular U1A -PIE complex. a, Top and b, side stereo views of a low energy structure of the trimolecular complex and c, superposition of 13 converged structures.
Figure 6.
Figure 6. Close-up view of the intermolecular hydrophobic interactions involving Ile 93, Met 97, Gly 99, Thr 100 and Val 102. a, A low energy structure and b, superposition of 13 converged structures.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 329-335) 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.  
21419778 D.Anunciado, A.Dhar, M.Gruebele, and A.M.Baranger (2011).
Multistep kinetics of the U1A-SL2 RNA complex dissociation.
  J Mol Biol, 408, 896-908.  
20554048 A.R.Ferré-D'Amaré (2010).
Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs.
  Methods, 52, 159-167.  
20223209 C.D.Cukier, and A.Ramos (2010).
Creating a twin STAR.
  Structure, 18, 279-280.  
20044349 S.Millevoi, and S.Vagner (2010).
Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation.
  Nucleic Acids Res, 38, 2757-2774.  
19522502 G.M.Clore, and J.Iwahara (2009).
Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes.
  Chem Rev, 109, 4108-4139.  
18929141 G.Z.Sowa, and P.Z.Qin (2008).
Site-directed spin labeling studies on nucleic acid structure and dynamics.
  Prog Nucleic Acid Res Mol Biol, 82, 147-197.  
18560762 H.E.Lindfors, P.E.de Koning, J.W.Drijfhout, B.Venezia, and M.Ubbink (2008).
Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR.
  J Biomol NMR, 41, 157-167.  
19043415 M.Teplova, and D.J.Patel (2008).
Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1.
  Nat Struct Mol Biol, 15, 1343-1351.
PDB codes: 3d2n 3d2q 3d2s
17452349 A.Busch, and R.Backofen (2007).
INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints.
  Nucleic Acids Res, 35, W310-W313.  
17913493 G.M.Clore, C.Tang, and J.Iwahara (2007).
Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement.
  Curr Opin Struct Biol, 17, 603-616.  
17084097 J.Iwahara, C.Tang, and G.Marius Clore (2007).
Practical aspects of (1)H transverse paramagnetic relaxation enhancement measurements on macromolecules.
  J Magn Reson, 184, 185-195.  
17980039 Y.Benitex, and A.M.Baranger (2007).
Recognition of essential purines by the U1A protein.
  BMC Biochem, 8, 22.  
16834346 B.L.Kormos, A.M.Baranger, and D.L.Beveridge (2006).
Do collective atomic fluctuations account for cooperative effects? Molecular dynamics studies of the U1A-RNA complex.
  J Am Chem Soc, 128, 8992-8993.  
16935886 E.Jankowsky, and H.Bowers (2006).
Remodeling of ribonucleoprotein complexes with DExH/D RNA helicases.
  Nucleic Acids Res, 34, 4181-4188.  
16556937 H.A.Bowers, P.A.Maroney, M.E.Fairman, B.Kastner, R.Lührmann, T.W.Nilsen, and E.Jankowsky (2006).
Discriminatory RNP remodeling by the DEAD-box protein DED1.
  RNA, 12, 903-912.  
16794580 J.M.Pérez-Cañadillas (2006).
Grabbing the message: structural basis of mRNA 3'UTR recognition by Hrp1.
  EMBO J, 25, 3167-3178.
PDB code: 2cjk
16987907 M.Hiller, R.Pudimat, A.Busch, and R.Backofen (2006).
Using RNA secondary structures to guide sequence motif finding towards single-stranded regions.
  Nucleic Acids Res, 34, e117.  
16738410 M.J.Law, A.J.Rice, P.Lin, and I.A.Laird-Offringa (2006).
The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA.
  RNA, 12, 1168-1178.  
16407334 M.J.Law, M.E.Linde, E.J.Chambers, C.Oubridge, P.S.Katsamba, L.Nilsson, I.S.Haworth, and I.A.Laird-Offringa (2006).
The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA.
  Nucleic Acids Res, 34, 275-285.  
16698546 N.Dobson, G.Dantas, D.Baker, and G.Varani (2006).
High-resolution structural validation of the computational redesign of human U1A protein.
  Structure, 14, 847-856.
PDB code: 2a3j
16982642 S.D.Auweter, F.C.Oberstrass, and F.H.Allain (2006).
Sequence-specific binding of single-stranded RNA: is there a code for recognition?
  Nucleic Acids Res, 34, 4943-4959.  
16362037 S.D.Auweter, R.Fasan, L.Reymond, J.G.Underwood, D.L.Black, S.Pitsch, and F.H.Allain (2006).
Molecular basis of RNA recognition by the human alternative splicing factor Fox-1.
  EMBO J, 25, 163-173.
PDB code: 2err
16278830 Y.Zhao, B.L.Kormos, D.L.Beveridge, and A.M.Baranger (2006).
Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface.
  Biopolymers, 81, 256-269.  
16075426 C.D.Mackereth, B.Simon, and M.Sattler (2005).
Extending the size of protein-RNA complexes studied by nuclear magnetic resonance spectroscopy.
  Chembiochem, 6, 1578-1584.  
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.  
15643449 R.Stefl, L.Skrisovska, and F.H.Allain (2005).
RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle.
  EMBO Rep, 6, 33-38.  
15659359 V.Cojocaru, S.Nottrott, R.Klement, and T.M.Jovin (2005).
The snRNP 15.5K protein folds its cognate K-turn RNA: a combined theoretical and biochemical study.
  RNA, 11, 197-209.  
15753311 V.Guallar, and K.W.Borrelli (2005).
A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding.
  Proc Natl Acad Sci U S A, 102, 3954-3959.  
15231733 C.L.Kielkopf, S.Lücke, and M.R.Green (2004).
U2AF homology motifs: protein recognition in the RRM world.
  Genes Dev, 18, 1513-1526.  
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.  
15192703 N.Leulliot, S.Quevillon-Cheruel, M.Graille, H.van Tilbeurgh, T.C.Leeper, K.S.Godin, T.E.Edwards, S.T.Sigurdsson, N.Rozenkrants, R.J.Nagel, M.Ares, and G.Varani (2004).
A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III.
  EMBO J, 23, 2468-2477.
PDB codes: 1t4n 1t4o
15121895 P.S.Klosterman, D.K.Hendrix, M.Tamura, S.R.Holbrook, and S.E.Brenner (2004).
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
  Nucleic Acids Res, 32, 2342-2352.  
15299008 Y.Iko, T.S.Kodama, N.Kasai, T.Oyama, E.H.Morita, T.Muto, M.Okumura, R.Fujii, T.Takumi, S.Tate, and K.Morikawa (2004).
Domain architectures and characterization of an RNA-binding protein, TLS.
  J Biol Chem, 279, 44834-44840.  
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
12670951 C.Phillips, and S.Gunderson (2003).
Sequences adjacent to the 5' splice site control U1A binding upstream of the IgM heavy chain secretory poly(A) site.
  J Biol Chem, 278, 22102-22111.  
12697817 F.Guan, D.Palacios, R.I.Hussein, and S.I.Gunderson (2003).
Determinants within an 18-amino-acid U1A autoregulatory domain that uncouple cooperative RNA binding, inhibition of polyadenylation, and homodimerization.
  Mol Cell Biol, 23, 3163-3172.  
12773396 J.M.Pérez Cañadillas, and G.Varani (2003).
Recognition of GU-rich polyadenylation regulatory elements by human CstF-64 protein.
  EMBO J, 22, 2821-2830.
PDB code: 1p1t
12615010 P.Romby, and M.Springer (2003).
Bacterial translational control at atomic resolution.
  Trends Genet, 19, 155-161.  
12466552 J.B.Tuite, J.C.Shiels, and A.M.Baranger (2002).
Substitution of an essential adenine in the U1A-RNA complex with a non-polar isostere.
  Nucleic Acids Res, 30, 5269-5275.  
11788718 J.C.Shiels, J.B.Tuite, S.J.Nolan, and A.M.Baranger (2002).
Investigation of a conserved stacking interaction in target site recognition by the U1A protein.
  Nucleic Acids Res, 30, 550-558.  
  12537566 M.P.Joachimiak, and F.E.Cohen (2002).
JEvTrace: refinement and variations of the evolutionary trace in JAVA.
  Genome Biol, 3, RESEARCH0077.  
11839494 T.M.Hall (2002).
Poly(A) tail synthesis and regulation: recent structural insights.
  Curr Opin Struct Biol, 12, 82-88.  
11226168 D.M.Campisi, V.Calabro, and A.D.Frankel (2001).
Structure-based design of a dimeric RNA-peptide complex.
  EMBO J, 20, 178-186.  
11141562 E.Jankowsky, C.H.Gross, S.Shuman, and A.M.Pyle (2001).
Active disruption of an RNA-protein interaction by a DExH/D RNA helicase.
  Science, 291, 121-125.  
11438677 H.Peled-Zehavi, J.A.Berglund, M.Rosbash, and A.D.Frankel (2001).
Recognition of RNA branch point sequences by the KH domain of splicing factor 1 (mammalian branch point binding protein) in a splicing factor complex.
  Mol Cell Biol, 21, 5232-5241.  
11179892 J.M.Pérez-Cañadillas, and G.Varani (2001).
Recent advances in RNA-protein recognition.
  Curr Opin Struct Biol, 11, 53-58.  
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
11118222 F.H.Allain, P.Bouvet, T.Dieckmann, and J.Feigon (2000).
Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin.
  EMBO J, 19, 6870-6881.
PDB code: 1fje
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.

 

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