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PDBsum entry 3dom

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protein Protein-protein interface(s) links
Transcription PDB id
3dom
Jmol
Contents
Protein chains
73 a.a. *
58 a.a. *
77 a.a. *
65 a.a. *
Waters ×97
* Residue conservation analysis
PDB id:
3dom
Name: Transcription
Title: Crystal structure of the complex between tfb5 and thE C-term domain of tfb2
Structure: RNA polymerase ii transcription factor b subunit chain: a, c. Fragment: c-terminal domain. Synonym: tfiih subunit tfb2, RNA polymerase ii transcriptio p52 subunit, RNA polymerase ii transcription factor b 52 kd general transcription and DNA repair factor iih subunit tfb engineered: yes. RNA polymerase ii transcription factor b subunit chain: b, d.
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Gene: tfb2. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: tfb5.
Resolution:
2.60Å     R-factor:   0.205     R-free:   0.261
Authors: D.E.Kainov,J.Cavarelli,J.M.Egly,A.Poterszman
Key ref:
D.E.Kainov et al. (2008). Structural basis for group A trichothiodystrophy. Nat Struct Biol, 15, 980-984. PubMed id: 19172752 DOI: 10.1038/nsmb.1478
Date:
04-Jul-08     Release date:   19-Aug-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q02939  (TFB2_YEAST) -  RNA polymerase II transcription factor B subunit 2
Seq:
Struc:
513 a.a.
73 a.a.
Protein chain
Pfam   ArchSchema ?
Q3E7C1  (TFB5_YEAST) -  RNA polymerase II transcription factor B subunit 5
Seq:
Struc:
72 a.a.
58 a.a.
Protein chain
Pfam   ArchSchema ?
Q02939  (TFB2_YEAST) -  RNA polymerase II transcription factor B subunit 2
Seq:
Struc:
513 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
Q3E7C1  (TFB5_YEAST) -  RNA polymerase II transcription factor B subunit 5
Seq:
Struc:
72 a.a.
65 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   4 terms 
  Biological process     phosphorylation of RNA polymerase II C-terminal domain   7 terms 
  Biochemical function     core RNA polymerase binding transcription factor activity     2 terms  

 

 
DOI no: 10.1038/nsmb.1478 Nat Struct Biol 15:980-984 (2008)
PubMed id: 19172752  
 
 
Structural basis for group A trichothiodystrophy.
D.E.Kainov, M.Vitorino, J.Cavarelli, A.Poterszman, J.M.Egly.
 
  ABSTRACT  
 
Patients with the rare neurodevelopmental repair syndrome known as group A trichothiodystrophy (TTD-A) carry mutations in the gene encoding the p8 subunit of the transcription and DNA repair factor TFIIH. Here we describe the crystal structure of a minimal complex between Tfb5, the yeast ortholog of p8, and the C-terminal domain of Tfb2, the yeast p52 subunit of TFIIH. The structure revealed that these two polypeptides adopt the same fold, forming a compact pseudosymmetric heterodimer via a beta-strand addition and coiled coils interactions between terminal alpha-helices. Furthermore, Tfb5 protects a hydrophobic surface in Tfb2 from solvent, providing a rationale for the influence of p8 in the stabilization of p52 and explaining why mutations that weaken p8-p52 interactions lead to a reduced intracellular TFIIH concentration and a defect in nucleotide-excision repair, a common feature of TTD cells.
 
  Selected figure(s)  
 
Figure 1.
(a) Ribbon representation of the Tfb2C–Tfb5 heterodimer (center), where Tfb2C is shown in brown and Tfb5 in blue. Details of intra- and intermolecular interactions are depicted in inserted panels I (for Tfb2C), II and III (for Tfb2C–Tfb5). (b) Representation of Tfb2C and Tfb5 monomers in the same orientation, highlighting the similar fold. The N helix from Tfb2 is not shown. (c) Schematic diagram of Tfb2C–Tfb5 interactions: dashed gray lines represent hydrogen bonds, black broken lines ion pairs and black solid lines van der Waals and hydrophobic contacts.
Figure 3.
(a) Wild-type (WT) yeast Tfb5 (residues 1–72), N (residues 16–72), C (residues 1–55) and L21P mutants were tested in dual excision (NER) and transcription (Tx) assays. Sizes of the incision products and the transcript are indicated. Recombinant IIH9 was omitted from the reactions (line 10) or replaced with TFIIH purified from human cells (line 11) in the control reactions. (b) Recombinant IIH9 complexes containing wild-type or mutant p52 lacking the p8-interacting domain were tested in dual excision and transcription assays. Increasing amounts of the complexes were incubated with or without recombinant human p8. (c) Western blot analysis of IIH9 complexes (left). Wild-type and mutant p52 were coexpressed in insect cells with p8 or with p8 and the other core TFIIH subunits (IIH6). Complexes were immunoprecipitated with anti-p52 antibody and analyzed for the presence of p8 (right).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2008, 15, 980-984) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20606254 D.E.Kainov, V.Cura, M.Vitorino, H.Nierengarten, P.Poussin, B.Kieffer, J.Cavarelli, and A.Poterszman (2010).
Structure determination of the minimal complex between Tfb5 and Tfb2, two subunits of the yeast transcription/DNA-repair factor TFIIH: a retrospective study.
  Acta Crystallogr D Biol Crystallogr, 66, 745-755.  
20017116 R.L.Rich, and D.G.Myszka (2010).
Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.
  J Mol Recognit, 23, 1.  
19809470 J.E.Cleaver, E.T.Lam, and I.Revet (2009).
Disorders of nucleotide excision repair: the genetic and molecular basis of heterogeneity.
  Nat Rev Genet, 10, 756-768.  
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