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PDBsum entry 2b22
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protein metals links
Biosynthetic protein PDB id
2b22

 

 

 

 

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Contents
Protein chain
29 a.a.
Metals
_NA ×2
Waters ×5
PDB id:
2b22
Name: Biosynthetic protein
Title: Antiparallel four-stranded coiled coil specified by a 3-3-1 hydrophobic heptad repeat
Structure: General control protein gcn4. Chain: a. Synonym: amino acid biosynthesis regulatory protein. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: gcn4, aas3, arg9. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.00Å     R-factor:   0.231     R-free:   0.276
Authors: Y.Deng,J.Liu,Q.Zheng,D.Eliezer,N.R.Kallenbach,M.Lu
Key ref:
Y.Deng et al. (2006). Antiparallel four-stranded coiled coil specified by a 3-3-1 hydrophobic heptad repeat. Structure, 14, 247-255. PubMed id: 16472744 DOI: 10.1016/j.str.2005.10.010
Date:
16-Sep-05     Release date:   31-Jan-06    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03069  (GCN4_YEAST) -  General control transcription factor GCN4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		281 a.a.
29 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 

 
DOI no: 10.1016/j.str.2005.10.010 Structure 14:247-255 (2006)
PubMed id: 16472744  
 
 
Antiparallel four-stranded coiled coil specified by a 3-3-1 hydrophobic heptad repeat.
Y.Deng, J.Liu, Q.Zheng, D.Eliezer, N.R.Kallenbach, M.Lu.
 
  ABSTRACT  
 
Coiled-coil sequences in proteins commonly share a seven-amino acid repeat with nonpolar side chains at the first (a) and fourth (d) positions. We investigate here the role of a 3-3-1 hydrophobic repeat containing nonpolar amino acids at the a, d, and g positions in determining the structures of coiled coils using mutants of the GCN4 leucine zipper dimerization domain. When three charged residues at the g positions in the parental sequence are replaced by nonpolar alanine or valine side chains, stable four-helix structures result. The X-ray crystal structures of the tetramers reveal antiparallel, four-stranded coiled coils in which the a, d, and g side chains interlock in a combination of knobs-into-knobs and knobs-into-holes packing. Interfacial interactions in a coiled coil can therefore be prescribed by hydrophobic-polar patterns beyond the canonical 3-4 heptad repeat. The results suggest that the conserved, charged residues at the g positions in the GCN4 leucine zipper can impart a negative design element to disfavor thermodynamically more stable, antiparallel tetramers.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Crystal Structure of the GCN4-pA Tetramer
(A) Lateral view of the tetramer. Red van der Waals surfaces identify residues at the a positions, green surfaces identify residues at the d positions, and yellow surfaces identify residues at the g positions. The N termini of helices A and B are indicated.
(B) Axial view of the tetramer. The green, yellow, and red van der Waals surfaces of the L6 (d), L30 (g), and V31 (a) side chains are depicted.
(C) Cross-section of the superhelix in the L20 (d) layer. The 1.5 Å 2F[o] – F[c] electron density map (contoured at 1.5σ) is shown with the refined molecular model.
(D) Helical wheel projection of residues 2–32 of the GCN4-pA tetramer. Heptad repeat positions are labeled a–g. The leucines at the d positions form the apolar interface of the tetramer. 		Figure 4.
Figure 4. Crystal Structure of the GCN4-pV Tetramer
(A) Lateral view of the tetramer. Red van der Waals surfaces identify residues at the a positions, green surfaces identify residues at the d positions, and yellow surfaces identify residues at the g positions. The N termini of helices A and B are indicated.
(B) Axial view of the tetramer. The green, yellow, and red van der Waals surfaces of the L6 (d), L30 (g), and V31 (a) side chains are depicted.
(C) Cross-section of the superhelix in the L20 (d) layer. The 2F[o] – F[c] electron density map at 1.2σ contour is shown with the refined molecular model.
(D) Superposition of the backbone conformations of the parallel GCN4-pIL tetramer (red) and the antiparallel GCN4-pA (green) and GCN4-pV (yellow) tetramers.
 
  The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 247-255) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20168298 A.Giamarchi, S.Feng, L.Rodat-Despoix, Y.Xu, E.Bubenshchikova, L.J.Newby, J.Hao, C.Gaudioso, M.Crest, A.N.Lupas, E.Honoré, M.P.Williamson, T.Obara, A.C.Ong, and P.Delmas (2010).
A polycystin-2 (TRPP2) dimerization domain essential for the function of heteromeric polycystin complexes.
  EMBO J, 29, 1176-1191.  
20027625 J.Diao (2010).
Crystal structure of a super leucine zipper, an extended two-stranded super long coiled coil.
  Protein Sci, 19, 319-326.
PDB code: 3i1g
20420519 S.Banta, I.R.Wheeldon, and M.Blenner (2010).
Protein engineering in the development of functional hydrogels.
  Annu Rev Biomed Eng, 12, 167-186.  
19805278 D.Albanesi, M.Martín, F.Trajtenberg, M.C.Mansilla, A.Haouz, P.M.Alzari, D.de Mendoza, and A.Buschiazzo (2009).
Structural plasticity and catalysis regulation of a thermosensor histidine kinase.
  Proc Natl Acad Sci U S A, 106, 16185-16190.
PDB codes: 3ehf 3ehh 3ehj 3gie 3gif 3gig
18545699 A.Surcel, D.Koshland, H.Ma, and R.T.Simpson (2008).
Cohesin interaction with centromeric minichromosomes shows a multi-complex rod-shaped structure.
  PLoS ONE, 3, e2453.  
18753631 D.N.Ho, N.C.Pomroy, J.A.Cuesta-Seijo, and G.G.Privé (2008).
Crystal structure of a self-assembling lipopeptide detergent at 1.20 A.
  Proc Natl Acad Sci U S A, 105, 12861-12866.
PDB code: 3cay
18555680 G.Grigoryan, and A.E.Keating (2008).
Structural specificity in coiled-coil interactions.
  Curr Opin Struct Biol, 18, 477-483.  
18782578 Y.Fujiwara, and D.L.Minor (2008).
X-ray crystal structure of a TRPM assembly domain reveals an antiparallel four-stranded coiled-coil.
  J Mol Biol, 383, 854-870.
PDB code: 3e7k
17189475 Y.Deng, Q.Zheng, J.Liu, C.S.Cheng, N.R.Kallenbach, and M.Lu (2007).
Self-assembly of coiled-coil tetramers in the 1.40 A structure of a leucine-zipper mutant.
  Protein Sci, 16, 323-328.
PDB code: 2nrn
16959572 M.Hulko, F.Berndt, M.Gruber, J.U.Linder, V.Truffault, A.Schultz, J.Martin, J.E.Schultz, A.N.Lupas, and M.Coles (2006).
The HAMP domain structure implies helix rotation in transmembrane signaling.
  Cell, 126, 929-940.  
16698550 Y.Deng, J.Liu, Q.Zheng, W.Yong, and M.Lu (2006).
Structures and polymorphic interactions of two heptad-repeat regions of the SARS virus S2 protein.
  Structure, 14, 889-899.
PDB codes: 1zv7 1zv8 1zva 1zvb
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.

 

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