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PDBsum entry 1rkj

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protein dna_rna links
Transcription/RNA PDB id
1rkj
Jmol
Contents
Protein chain
175 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
1rkj
Name: Transcription/RNA
Title: Solution structure of the complex formed by the two n- terminal RNA-binding domains of nucleolin and a pre-rrna target
Structure: Nucleolin. Chain: a. Synonym: protein c23. Engineered: yes. 5'- r( Gp Gp Ap Up Gp Cp Cp Up Cp Cp Cp Gp Ap Gp Up Gp Cp Ap Up Cp C)-3'. Chain: b. Engineered: yes
Source: Mesocricetus auratus. Golden hamster. Organism_taxid: 10036. Gene: ncl. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the RNA was chemically synthesized. The sequence of the RNA is naturally found in the 5' ets of
NMR struc: 14 models
Authors: C.Johansson,L.D.Finger,L.Trantirek,T.D.Mueller,S.Kim, I.A.Laird-Offringa,J.Feigon
Key ref:
C.Johansson et al. (2004). Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target. J Mol Biol, 337, 799-816. PubMed id: 15033352 DOI: 10.1016/j.jmb.2004.01.056
Date:
21-Nov-03     Release date:   27-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08199  (NUCL_MESAU) -  Nucleolin
Seq:
Struc:
 
Seq:
Struc:
714 a.a.
175 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

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

 

 
DOI no: 10.1016/j.jmb.2004.01.056 J Mol Biol 337:799-816 (2004)
PubMed id: 15033352  
 
 
Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target.
C.Johansson, L.D.Finger, L.Trantirek, T.D.Mueller, S.Kim, I.A.Laird-Offringa, J.Feigon.
 
  ABSTRACT  
 
Nucleolin is a 70 kDa multidomain protein involved in several steps of eukaryotic ribosome biogenesis. In vitro selection in combination with mutagenesis and structural analysis identified binding sites in pre-rRNA with the consensus (U/G)CCCG(A/G) in the context of a hairpin structure, the nucleolin recognition element (NRE). The central region of the protein contains four tandem RNA-binding domains (RBDs), of which the first two are responsible for the RNA-binding specificity and affinity for NREs. Here, we present the solution structure of the 28 kDa complex formed by the two N-terminal RNA-binding domains of nucleolin (RBD12) and a natural pre-rRNA target, b2NRE. The structure demonstrates that the sequence-specific recognition of the pre-rRNA NRE is achieved by intermolecular hydrogen bonds and stacking interactions involving mainly the beta-sheet surfaces of the two RBDs and the linker residues. A comparison with our previously determined NMR structure of RBD12 in complex with an in vitro selected RNA target, sNRE, shows that although the sequence-specific recognition of the loop consensus nucleotides is the same in the two complexes, they differ in several aspects. While the protein makes numerous specific contacts to the non-consensus nucleotides in the loop E motif (S-turn) in the upper part of the sNRE stem, nucleolin RBD12 contacts only consensus nucleotides in b2NRE. The absence of these upper stem contacts from the RBD12/b2NRE complex results in a much less stable complex, as demonstrated by kinetic analyses. The role of the loop E motif in high-affinity binding is supported by gel-shift analyses with a series of sNRE mutants. The less stable interaction of RBD12 with the natural RNA target is consistent with the proposed role of nucleolin as a chaperone that interacts transiently with pre-rRNA to prevent misfolding.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Superposition of the ensemble of the 14 lowest-energy structures of the nucleolin RBD12/b2NRE complex. a, The nucleolin RBD12/b2NRE complex showing the backbone superposition of RBD12 (11-170) and the lowest-energy structure of b2NRE. b, Heavy-atom superposition (nucleotides 2-15, 17-21) of b2NRE and the lowest-energy RBD12 structure shown in ribbon representation. c, Superposition of backbone atoms of RBD12 (T11-Y170) and all heavy atoms of the b2NRE loop (nucleotides 8-15) (Table 1). RBD1 is shown in blue, the linker in red, RBD2 in green, and b2NRE in orange.
Figure 5.
Figure 5. Global view of the nucleolin RBD12/b2NRE complex structure. The lowest-energy structure is shown. a, Stereoview of the complex, showing b2NRE and nucleolin RBD12 in stick and ribbon representations, respectively. The b2NRE (orange) loop is sandwiched between the two RBDs, with RBD1 (blue) interacting with nucleotides at the 3' side of the RNA (C12, G13 and A14) and RBD2 (green) contacting nucleotides of the 5' side (U9 and C10). The linker (red) spans the major groove of the loop. Some of the amino acid side-chains (green) at the interface (Y58, F56, K94, R127, Y140) are shown in stick representation. b, Surface representation of the whole complex. The side-chains of linker residues K95 and R97 (red), pack closely against the RNA. The view and color scheme is the same as in a. c, Surface representation of the whole complex with the molecule turned vert, similar 180° relative to b, showing the two holes in the RNA loop. The linker residue K94 (red) inserts into the upper hole, whereas R97 packs against the lower hole, possibly involved in water-mediated interactions with the RNA.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 337, 799-816) copyright 2004.  
  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.  
21333656 J.Wang, and E.P.Nikonowicz (2011).
Solution structure of the K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-box leader RNA.
  J Mol Biol, 408, 99.  
19838329 J.G.Routsias, N.Kyriakidis, M.Latreille, and A.G.Tzioufas (2010).
RNA recognition motif (RRM) of La/SSB: the bridge for interparticle spreading of autoimmune response to U1-RNP.
  Mol Med, 16, 19-26.  
20110252 J.Wang, T.M.Henkin, and E.P.Nikonowicz (2010).
NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA.
  Nucleic Acids Res, 38, 3388-3398.
PDB code: 2khy
20479262 Q.Yang, G.M.Gilmartin, and S.Doublié (2010).
Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing.
  Proc Natl Acad Sci U S A, 107, 10062-10067.
PDB codes: 3mdg 3mdi
20376532 S.Arumugam, M.C.Miller, J.Maliekal, P.J.Bates, J.O.Trent, and A.N.Lane (2010).
Solution structure of the RBD1,2 domains from human nucleolin.
  J Biomol NMR, 47, 79-83.
PDB code: 2krr
18515081 A.Cléry, M.Blatter, and F.H.Allain (2008).
RNA recognition motifs: boring? Not quite.
  Curr Opin Struct Biol, 18, 290-298.  
16679019 S.Curry, and M.R.Conte (2006).
A terminal affair: 3'-end recognition by the human La protein.
  Trends Biochem Sci, 31, 303-305.  
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.  
16611943 S.Wang, Y.Hu, M.T.Overgaard, F.V.Karginov, O.C.Uhlenbeck, and D.B.McKay (2006).
The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold.
  RNA, 12, 959-967.
PDB code: 2g0c
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.  
16122968 A.M.Bonvin, R.Boelens, and R.Kaptein (2005).
NMR analysis of protein interactions.
  Curr Opin Chem Biol, 9, 501-508.  
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.  
15914668 M.J.Law, E.J.Chambers, P.S.Katsamba, I.S.Haworth, and I.A.Laird-Offringa (2005).
Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction.
  Nucleic Acids Res, 33, 2917-2928.  
16252250 R.L.Rich, and D.G.Myszka (2005).
Survey of the year 2004 commercial optical biosensor literature.
  J Mol Recognit, 18, 431-478.  
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.  
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.