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PDBsum entry 2f9d
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protein Protein-protein interface(s) links
RNA binding protein PDB id
2f9d

 

 

 

 

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Contents
Protein chains
114 a.a. *
39 a.a. *
Waters ×67
* Residue conservation analysis
PDB id:
2f9d
Name: RNA binding protein
Title: 2.5 angstrom resolution structure of the spliceosomal protein p14 bound to region of sf3b155
Structure: Pre-mRNA branch site protein p14. Chain: a, b. Synonym: sf3b 14 kda subunit. Engineered: yes. Splicing factor 3b subunit 1. Chain: p, q. Fragment: residues: 373-415. Synonym: spliceosome associated protein 155, sap 155, sf3b155, pre- mRNA splicing factor sf3b 155 kda subunit.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sf3b14. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Gene: sf3b1, sap155. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.224     R-free:   0.276
Authors: M.J.Schellenberg,R.A.Edwards,D.B.Ritchie,J.N.M.Glover,A.M.Macmillan
Key ref:
M.J.Schellenberg et al. (2006). Crystal structure of a core spliceosomal protein interface. Proc Natl Acad Sci U S A, 103, 1266-1271. PubMed id: 16432215 DOI: 10.1073/pnas.0508048103
Date:
05-Dec-05     Release date:   24-Jan-06    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9Y3B4  (SF3B6_HUMAN) -  Splicing factor 3B subunit 6 from Homo sapiens
Seq:
Struc: 		125 a.a.
114 a.a.
Protein chains
Pfam   ArchSchema ?
O75533  (SF3B1_HUMAN) -  Splicing factor 3B subunit 1 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1304 a.a.
39 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1073/pnas.0508048103 Proc Natl Acad Sci U S A 103:1266-1271 (2006)
PubMed id: 16432215  
 
 
Crystal structure of a core spliceosomal protein interface.
M.J.Schellenberg, R.A.Edwards, D.B.Ritchie, O.A.Kent, M.M.Golas, H.Stark, R.Lührmann, J.N.Glover, A.M.Macmillan.
 
  ABSTRACT  
 
The precise excision of introns from precursor mRNAs (pre-mRNAs) in eukaryotes is accomplished by the spliceosome, a complex assembly containing five small nuclear ribonucleoprotein (snRNP) particles. Human p14, a component of the spliceosomal U2 and U11/U12 snRNPs, has been shown to associate directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. Here we report the 2.5-A crystal structure of a complex containing p14 and a peptide derived from the p14-associated U2 snRNP component SF3b155. p14 contains an RNA recognition motif (RRM), the surface of which is largely occluded by a C-terminal alpha-helix and a portion of the SF3b155 peptide. An analysis of RNA.protein crosslinking to wild-type and mutant p14 shows that the branch adenosine directly interacts with a conserved aromatic within a pocket on the surface of the complex. This result, combined with a comparison of the structure with known RRMs and pseudoRRMs as well as model-building by using the electron cryomicroscopy structure of a spliceosomal U11/U12 di-snRNP, suggests that p14.SF3b155 presents a noncanonical surface for RNA recognition at the heart of the mammalian spliceosome.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Details of p14·SF3b155 interface. (A) Hydrophobic core of the p14·SF3b155 interface. p14 is colored yellow, and SF3b155 peptide is colored blue. (B) Hydrogen-bonding network and salt bridges surrounding the hydrophobic core. p14 is colored yellow, and SF3b155 peptide is colored blue. Hydrogen bonds involved in secondary structural elements are omitted. (C) Surface representation of the p14·SF3b155 complex showing Y22 of RNP2 exposed within a surface pocket surrounded by conserved basic residues. p14 is shaded light gray, SF3b is shaded dark gray, Y22 is colored yellow, and R24, R57, R96, and K100 are colored blue. 		Figure 4.
Fig. 4. Comparison between p14·SF3b155 peptide surface and structures of U1A and U2AF65 RRM3. (A)(Left) NMR structure of free U1A with C-terminal helix (in yellow) positioned across RNA-binding surface (19). (Middle) X-ray structure of free U1A showing C-terminal helix rotated to unmask the RNA binding surface (20). (Right) Structure of p14·SF3b155 complex showing C-terminal helices of p14 and Sf3b155 peptide (in yellow). RNP1 and RNP2 are colored red and blue, respectively. (B) Representation of surface charges of p14·SF3b155 and U2AF homology motif (RRM3) of U2AF^65. The color scheme is as follows: blue, basic; red, acidic; white, neutral.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21295486 Q.Yang, M.Coseno, G.M.Gilmartin, and S.Doublié (2011).
Crystal structure of a human cleavage factor CFI(m)25/CFI(m)68/RNA complex provides an insight into poly(A) site recognition and RNA looping.
  Structure, 19, 368-377.
PDB codes: 3q2s 3q2t
20711187 C.D.Cukier, D.Hollingworth, S.R.Martin, G.Kelly, I.Díaz-Moreno, and A.Ramos (2010).
Molecular basis of FIR-mediated c-myc transcriptional control.
  Nat Struct Mol Biol, 17, 1058-1064.  
19401679 C.Taxis, G.Stier, R.Spadaccini, and M.Knop (2009).
Efficient protein depletion by genetically controlled deprotection of a dormant N-degron.
  Mol Syst Biol, 5, 267.  
  19119309 G.Boldina, A.Ivashchenko, and M.Régnier (2009).
Using profiles based on nucleotide hydrophobicity to define essential regions for splicing.
  Int J Biol Sci, 5, 13-19.  
19523901 J.H.Lee, E.S.Rangarajan, S.D.Yogesha, and T.Izard (2009).
Raver1 interactions with vinculin and RNA suggest a feed-forward pathway in directing mRNA to focal adhesions.
  Structure, 17, 833-842.
PDB codes: 3h2u 3h2v
19239890 M.C.Wahl, C.L.Will, and R.Lührmann (2009).
The spliceosome: design principles of a dynamic RNP machine.
  Cell, 136, 701-718.  
18515081 A.Cléry, M.Blatter, and F.H.Allain (2008).
RNA recognition motifs: boring? Not quite.
  Curr Opin Struct Biol, 18, 290-298.  
18621724 A.M.van Roon, N.M.Loening, E.Obayashi, J.C.Yang, A.J.Newman, H.Hernández, K.Nagai, and D.Neuhaus (2008).
Solution structure of the U2 snRNP protein Rds3p reveals a knotted zinc-finger motif.
  Proc Natl Acad Sci U S A, 105, 9621-9626.
PDB code: 2k0a
19000813 J.Sperling, M.Azubel, and R.Sperling (2008).
Structure and function of the Pre-mRNA splicing machine.
  Structure, 16, 1605-1615.  
18076038 K.Kuwasako, N.Dohmae, M.Inoue, M.Shirouzu, S.Taguchi, P.Güntert, B.Séraphin, Y.Muto, and S.Yokoyama (2008).
Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses.
  Proteins, 71, 1617-1636.  
18550358 M.S.Jurica (2008).
Detailed close-ups and the big picture of spliceosomes.
  Curr Opin Struct Biol, 18, 315-320.  
18588901 V.Manceau, C.L.Kielkopf, A.Sobel, and A.Maucuer (2008).
Different requirements of the kinase and UHM domains of KIS for its nuclear localization and binding to splicing factors.
  J Mol Biol, 381, 748-762.  
17652325 E.Kühn-Hölsken, O.Dybkov, B.Sander, R.Lührmann, and H.Urlaub (2007).
Improved identification of enriched peptide RNA cross-links from ribonucleoprotein particles (RNPs) by mass spectrometry.
  Nucleic Acids Res, 35, e95.  
17360628 M.D.Ohi, L.Ren, J.S.Wall, K.L.Gould, and T.Walz (2007).
Structural characterization of the fission yeast U5.U2/U6 spliceosome complex.
  Proc Natl Acad Sci U S A, 104, 3195-3200.  
17570818 O.Fedorova, and N.Zingler (2007).
Group II introns: structure, folding and splicing mechanism.
  Biol Chem, 388, 665-678.  
17574835 S.Valadkhan (2007).
The spliceosome: caught in a web of shifting interactions.
  Curr Opin Struct Biol, 17, 310-315.  
16885237 C.Dominguez, and F.H.Allain (2006).
NMR structure of the three quasi RNA recognition motifs (qRRMs) of human hnRNP F and interaction studies with Bcl-x G-tract RNA: a novel mode of RNA recognition.
  Nucleic Acids Res, 34, 3634-3645.
PDB codes: 2hgl 2hgm 2hgn
16689644 H.Stark, and R.Lührmann (2006).
Cryo-electron microscopy of spliceosomal components.
  Annu Rev Biophys Biomol Struct, 35, 435-457.  
16973435 S.Hamill, and A.M.Pyle (2006).
The receptor for branch-site docking within a group II intron active site.
  Mol Cell, 23, 831-840.  
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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