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PDBsum entry 1zij
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protein Protein-protein interface(s) links
Leucine zipper PDB id
1zij

 

 

 

 

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Contents
Protein chains
34 a.a.
Waters ×34
PDB id:
1zij
Name: Leucine zipper
Title: Gcn4-leucine zipper core mutant asn16aba in the trimeric state
Structure: General control protein gcn4. Chain: a, b, c. Synonym: gcn4. Engineered: yes. Mutation: yes. Other_details: this structure is in the trimeric state
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Biol. unit: Trimer (from PQS)
Resolution:
2.00Å     R-factor:   0.184    
Authors: L.Gonzalez Junior,R.A.Brown,D.Richardson,T.Alber
Key ref: L.Gonzalez et al. (1996). Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism. Nat Struct Biol, 3, 1002-1009. PubMed id: 8946853
Date:
30-Oct-96     Release date:   07-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P03069  (GCN4_YEAST) -  General control transcription factor GCN4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		281 a.a.
33 a.a.*
Key:    Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
Nat Struct Biol 3:1002-1009 (1996)
PubMed id: 8946853  
 
 
Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism.
L.Gonzalez, R.A.Brown, D.Richardson, T.Alber.
 
  ABSTRACT  
 
Each protein sequence generally adopts a single native fold, but the sequence features that confer structural uniqueness are not well understood. To define the basis for structural heterogeneity, we determined the high resolution X-ray crystal structures of a single GCN4 leucine-zipper mutant (Asn 16 to aminobutyric acid) in both dimeric and trimeric coiled-coil conformations. The mutant sequence is accommodated in two distinct structures by forming similarly-shaped packing surfaces with different sets of atoms. The trimer structure, in comparison to a previously-characterized trimeric mutant with substitutions in eight core residues, shows that the twist of individual helices and the helix-helix crossing angles can vary significantly to produce the most favoured packing arrangement.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21183075 F.Fiumara, L.Fioriti, E.R.Kandel, and W.A.Hendrickson (2010).
Essential role of coiled coils for aggregation and activity of Q/N-rich prions and PolyQ proteins.
  Cell, 143, 1121-1135.  
19693805 Q.Xu, and D.L.Minor (2009).
Crystal structure of a trimeric form of the K(V)7.1 (KCNQ1) A-domain tail coiled-coil reveals structural plasticity and context dependent changes in a putative coiled-coil trimerization motif.
  Protein Sci, 18, 2100-2114.
PDB codes: 3hfc 3hfe
19627992 R.S.Hodges, J.Mills, S.McReynolds, J.P.Kirwan, B.Tripet, and D.Osguthorpe (2009).
Identification of a unique "stability control region" that controls protein stability of tropomyosin: A two-stranded alpha-helical coiled-coil.
  J Mol Biol, 392, 747-762.  
18704948 S.S.Pendley, Y.B.Yu, and T.E.Cheatham (2009).
Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils.
  Proteins, 74, 612-629.  
17609383 D.S.Touw, C.E.Nordman, J.A.Stuckey, and V.L.Pecoraro (2007).
Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled coils.
  Proc Natl Acad Sci U S A, 104, 11969-11974.
PDB code: 2jgo
16584182 M.K.Yadav, L.J.Leman, D.J.Price, C.L.Brooks, C.D.Stout, and M.R.Ghadiri (2006).
Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution.
  Biochemistry, 45, 4463-4473.
PDB codes: 1w5h 1w5j 1w5k 1w5l 2cce 2ccf 2ccn
16008357 M.K.Yadav, J.E.Redman, L.J.Leman, J.M.Alvarez-Gutiérrez, Y.Zhang, C.D.Stout, and M.R.Ghadiri (2005).
Structure-based engineering of internal cavities in coiled-coil peptides.
  Biochemistry, 44, 9723-9732.
PDB codes: 1unt 1unu 1unv 1unw 1unx 1uny 1unz 1uo0 1uo1 1uo2 1uo3 1uo4 1uo5 1w5g 1w5i 2bni
15340167 A.L.Lomize, I.D.Pogozheva, and H.I.Mosberg (2004).
Quantification of helix-helix binding affinities in micelles and lipid bilayers.
  Protein Sci, 13, 2600-2612.  
14759261 J.H.Fong, A.E.Keating, and M.Singh (2004).
Predicting specificity in bZIP coiled-coil protein interactions.
  Genome Biol, 5, R11.  
14752198 J.Holton, and T.Alber (2004).
Automated protein crystal structure determination using ELVES.
  Proc Natl Acad Sci U S A, 101, 1537-1542.
PDB codes: 1rb1 1rb4 1rb5 1rb6 3k7z
14760737 J.M.Mason, and K.M.Arndt (2004).
Coiled coil domains: stability, specificity, and biological implications.
  Chembiochem, 5, 170-176.  
15010542 N.Pokala, and T.M.Handel (2004).
Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation.
  Protein Sci, 13, 925-936.  
15345544 T.Stockner, W.L.Ash, J.L.MacCallum, and D.P.Tieleman (2004).
Direct simulation of transmembrane helix association: role of asparagines.
  Biophys J, 87, 1650-1656.  
12829817 C.Song, and E.Hunter (2003).
Variable sensitivity to substitutions in the N-terminal heptad repeat of Mason-Pfizer monkey virus transmembrane protein.
  J Virol, 77, 7779-7785.  
12649422 W.F.DeGrado, H.Gratkowski, and J.D.Lear (2003).
How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles.
  Protein Sci, 12, 647-665.  
12202385 H.Gratkowski, Q.H.Dai, A.J.Wand, W.F.DeGrado, and J.D.Lear (2002).
Cooperativity and specificity of association of a designed transmembrane peptide.
  Biophys J, 83, 1613-1619.  
11939781 K.M.Campbell, A.J.Sholders, and K.J.Lumb (2002).
Contribution of buried lysine residues to the oligomerization specificity and stability of the fos coiled coil.
  Biochemistry, 41, 4866-4871.  
11679589 L.J.Tai, S.M.McFall, K.Huang, B.Demeler, S.G.Fox, K.Brubaker, I.Radhakrishnan, and R.I.Morimoto (2002).
Structure-function analysis of the heat shock factor-binding protein reveals a protein composed solely of a highly conserved and dynamic coiled-coil trimerization domain.
  J Biol Chem, 277, 735-745.  
11371197 D.L.Akey, V.N.Malashkevich, and P.S.Kim (2001).
Buried polar residues in coiled-coil interfaces.
  Biochemistry, 40, 6352-6360.
PDB codes: 1ij0 1ij1 1ij2 1ij3
11266591 H.Zhu, S.A.Celinski, J.M.Scholtz, and J.C.Hu (2001).
An engineered leucine zipper a position mutant with an unusual three-state unfolding pathway.
  Protein Sci, 10, 24-33.  
11714921 K.Dutta, A.Alexandrov, H.Huang, and S.M.Pascal (2001).
pH-induced folding of an apoptotic coiled coil.
  Protein Sci, 10, 2531-2540.  
11317312 Y.Tang, G.Ghirlanda, W.A.Petka, T.Nakajima, W.F.DeGrado, and D.A.Tirrell (2001).
Fluorinated Coiled-Coil Proteins Prepared In Vivo Display Enhanced Thermal and Chemical Stability This work was supported by a grant from the U.S. Army Research Office. Y. Tang is supported by a Whitaker Graduate Research Fellowship. We thank Dr. Gary Hathaway for performing matrix-assisted laser desorption/ionization analyses.
  Angew Chem Int Ed Engl, 40, 1494-1496.  
10913284 M.J.Pandya, G.M.Spooner, M.Sunde, J.R.Thorpe, A.Rodger, and D.N.Woolfson (2000).
Sticky-end assembly of a designed peptide fiber provides insight into protein fibrillogenesis.
  Biochemistry, 39, 8728-8734.  
10775580 R.J.Center, P.L.Earl, J.Lebowitz, P.Schuck, and B.Moss (2000).
The human immunodeficiency virus type 1 gp120 V2 domain mediates gp41-independent intersubunit contacts.
  J Virol, 74, 4448-4455.  
  10595534 K.Wagschal, B.Tripet, P.Lavigne, C.Mant, and R.S.Hodges (1999).
The role of position a in determining the stability and oligomerization state of alpha-helical coiled coils: 20 amino acid stability coefficients in the hydrophobic core of proteins.
  Protein Sci, 8, 2312-2329.  
10090742 R.Peteranderl, M.Rabenstein, Y.K.Shin, C.W.Liu, D.E.Wemmer, D.S.King, and H.C.Nelson (1999).
Biochemical and biophysical characterization of the trimerization domain from the heat shock transcription factor.
  Biochemistry, 38, 3559-3569.  
  10210186 S.Nautiyal, and T.Alber (1999).
Crystal structure of a designed, thermostable, heterotrimeric coiled coil.
  Protein Sci, 8, 84-90.
PDB code: 1bb1
10545330 V.A.Kostyuchenko, G.A.Navruzbekov, L.P.Kurochkina, S.V.Strelkov, V.V.Mesyanzhinov, and M.G.Rossmann (1999).
The structure of bacteriophage T4 gene product 9: the trigger for tail contraction.
  Structure, 7, 1213-1222.
PDB codes: 1qex 1s2e
10872466 W.F.DeGrado, C.M.Summa, V.Pavone, F.Nastri, and A.Lombardi (1999).
De novo design and structural characterization of proteins and metalloproteins.
  Annu Rev Biochem, 68, 779-819.  
10220324 W.Shu, H.Ji, and M.Lu (1999).
Trimerization specificity in HIV-1 gp41: analysis with a GCN4 leucine zipper model.
  Biochemistry, 38, 5378-5385.
PDB code: 1ce0
  10422826 Z.S.Hendsch, and B.Tidor (1999).
Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding.
  Protein Sci, 8, 1381-1392.  
9565750 J.P.Schneider, A.Lombardi, and W.F.DeGrado (1998).
Analysis and design of three-stranded coiled coils and three-helix bundles.
  Fold Des, 3, R29-R40.  
  9605327 N.Liu, C.Deillon, S.Klauser, B.Gutte, and R.M.Thomas (1998).
Synthesis, physicochemical characterization, and crystallization of a putative retro-coiled coil.
  Protein Sci, 7, 1214-1220.  
9442881 J.J.Falke, R.B.Bass, S.L.Butler, S.A.Chervitz, and M.A.Danielson (1997).
The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes.
  Annu Rev Cell Dev Biol, 13, 457-512.  
9233786 K.Beck, J.E.Gambee, A.Kamawal, and H.P.Bächinger (1997).
A single amino acid can switch the oligomerization state of the alpha-helical coiled-coil domain of cartilage matrix protein.
  EMBO J, 16, 3767-3777.  
9407066 M.A.Danielson, R.B.Bass, and J.J.Falke (1997).
Cysteine and disulfide scanning reveals a regulatory alpha-helix in the cytoplasmic domain of the aspartate receptor.
  J Biol Chem, 272, 32878-32888.  
9261070 Y.Tao, S.V.Strelkov, V.V.Mesyanzhinov, and M.G.Rossmann (1997).
Structure of bacteriophage T4 fibritin: a segmented coiled coil and the role of the C-terminal domain.
  Structure, 5, 789-798.
PDB code: 1aa0
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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