PDBsum entry 2hgh

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protein dna_rna metals links
Transcription/RNA PDB id
Protein chain
87 a.a. *
_ZN ×3
* Residue conservation analysis
PDB id:
Name: Transcription/RNA
Title: Transcription factor iiia zinc fingers 4-6 bound to 5s rrna 55mer (nmr structure)
Structure: Transcription factor iiia. Chain: a. Fragment: zinc fingers 4-6 (residues 127-212). Synonym: factor a, tfiiia, s-tfiiia/o-tfiiia. Engineered: yes. 55-mer. Chain: b. Engineered: yes
Source: Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: RNA was synthesized by in vitro transcription from linearized puc18 plasmid containing the 55mer sequence and the primer binding site for t7 RNA
NMR struc: 20 models
Authors: B.M.Lee
Key ref:
B.M.Lee et al. (2006). Induced fit and "lock and key" recognition of 5S RNA by zinc fingers of transcription factor IIIA. J Mol Biol, 357, 275-291. PubMed id: 16405997 DOI: 10.1016/j.jmb.2005.12.010
27-Jun-06     Release date:   01-Aug-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P03001  (TF3A_XENLA) -  Transcription factor IIIA
366 a.a.
87 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     nucleic acid binding     2 terms  


DOI no: 10.1016/j.jmb.2005.12.010 J Mol Biol 357:275-291 (2006)
PubMed id: 16405997  
Induced fit and "lock and key" recognition of 5S RNA by zinc fingers of transcription factor IIIA.
B.M.Lee, J.Xu, B.K.Clarkson, M.A.Martinez-Yamout, H.J.Dyson, D.A.Case, J.M.Gottesfeld, P.E.Wright.
Transcription factor IIIA (TFIIIA) is a Cys2His2 zinc finger protein that regulates expression of the 5 S ribosomal RNA gene by binding specifically to the internal control element. TFIIIA also functions in transport and storage of 5 S RNA by binding directly to the RNA transcript. To obtain insights into the mechanism by which TFIIIA recognizes 5 S RNA, we determined the solution structure of the middle three zinc fingers bound to the central core of 5 S RNA. Finger 4 utilizes "lock and key" recognition to bind in the widened major groove of the pre-structured RNA loop E motif. This interaction is mediated by direct hydrogen bonding interactions with bases. In contrast, recognition of loop A, a flexible junction of three helices, occurs by an induced fit mechanism that involves reorganization of the conserved CAUA motif and structuring of the finger 5-finger 6 interface to form a complementary RNA binding surface.
  Selected figure(s)  
Figure 4.
Figure 4. Structure of the complex of zf46 with the 55mer RNA. (a) The 20 lowest energy structures superimposed on all heavy atoms of residues 105-188 of zf46 and all heavy atoms of the loop A, helix V and loop E regions of the RNA (nucleotides 3-10, 15-30, and 39-53, respectively). The backbone of the zinc fingers is colored orange for finger 4, green for finger 5 and magenta for finger 6. The side-chain heavy atoms of His119 in finger 4 and Trp177 in finger 6 are colored blue. The RNA backbone is colored red and the bases shown in grey. (b) Ribbon diagram of the lowest energy refined structure shown in the same orientation and color scheme, except that G:C and A:U bases are colored lilac and lime, respectively, and the zinc atoms are shown as gold colored spheres. The Figures were generated using MOLMOL.77
Figure 8.
Figure 8. Electrostatic surface representation of zf46 in the 55 mer complex. The structure shows the electropositive groove between fingers 5 and 6 that accommodates the CAUA motif (red backbone and pink bases) of 5 S RNA. The Figure was generated using MOLMOL.77
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 275-291) copyright 2006.  
  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.  
19179334 D.F.Estrada, D.M.Boudreaux, D.Zhong, S.C.St Jeor, and R.N.De Guzman (2009).
The Hantavirus Glycoprotein G1 Tail Contains Dual CCHC-type Classical Zinc Fingers.
  J Biol Chem, 284, 8654-8660.
PDB code: 2k9h
19474339 G.Zheng, X.J.Lu, and W.K.Olson (2009).
Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures.
  Nucleic Acids Res, 37, W240-W246.  
18790808 J.Acker, C.Ozanne, R.Kachouri-Lafond, C.Gaillardin, C.Neuvéglise, and C.Marck (2008).
Dicistronic tRNA-5S rRNA genes in Yarrowia lipolytica: an alternative TFIIIA-independent way for expression of 5S rRNA genes.
  Nucleic Acids Res, 36, 5832-5844.  
18253864 K.J.Brayer, and D.J.Segal (2008).
Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains.
  Cell Biochem Biophys, 50, 111-131.  
18286240 K.J.Brayer, S.Kulshreshtha, and D.J.Segal (2008).
The protein-binding potential of C2H2 zinc finger domains.
  Cell Biochem Biophys, 51, 9.  
18322526 M.Parisien, and F.Major (2008).
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data.
  Nature, 452, 51-55.  
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
18511071 S.M.Truhlar, E.Mathes, C.F.Cervantes, G.Ghosh, and E.A.Komives (2008).
Pre-folding IkappaBalpha alters control of NF-kappaB signaling.
  J Mol Biol, 380, 67-82.  
17610897 B.M.Lee, B.A.Buck-Koehntop, M.A.Martinez-Yamout, H.J.Dyson, and P.E.Wright (2007).
Embryonic neural inducing factor churchill is not a DNA-binding zinc finger protein: solution structure reveals a solvent-exposed beta-sheet and zinc binuclear cluster.
  J Mol Biol, 371, 1274-1289.
PDB code: 2jox
17473849 B.M.Lunde, C.Moore, and G.Varani (2007).
RNA-binding proteins: modular design for efficient function.
  Nat Rev Mol Cell Biol, 8, 479-490.  
17079314 J.M.Bailey, and W.E.Tapprich (2007).
Structure of the 5' nontranslated region of the coxsackievirus b3 genome: Chemical modification and comparative sequence analysis.
  J Virol, 81, 650-668.  
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.