PDBsum entry 1ih9

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Antibiotic PDB id
Protein chain
17 a.a.
PDB id:
Name: Antibiotic
Title: Nmr structure of zervamicin iib (peptaibol antibiotic) bound micelles
Structure: Zervamicin iib. Chain: a
Source: Emericellopsis salmosynnemata. Organism_taxid: 118885. Strain: 336 imi 58330
NMR struc: 20 models
Authors: Z.O.Shenkarev,T.A.Balasheva,R.G.Efremov,Z.A.Yakimenko, T.V.Ovchinnikova,J.Raap,A.S.Arseniev
Key ref: Z.O.Shenkarev et al. (2002). Spatial structure of zervamicin IIB bound to DPC micelles: implications for voltage-gating. Biophys J, 82, 762-771. PubMed id: 11806918
19-Apr-01     Release date:   13-Feb-02    
Go to PROCHECK summary

Protein chain
No UniProt id for this chain
Struc: 16 a.a.
Key:    Secondary structure


Biophys J 82:762-771 (2002)
PubMed id: 11806918  
Spatial structure of zervamicin IIB bound to DPC micelles: implications for voltage-gating.
Z.O.Shenkarev, T.A.Balashova, R.G.Efremov, Z.A.Yakimenko, T.V.Ovchinnikova, J.Raap, A.S.Arseniev.
Zervamicin IIB is a 16-amino acid peptaibol that forms voltage-dependent ion channels with multilevel conductance states in planar lipid bilayers and vesicular systems. The spatial structure of zervamicin IIB bound to dodecylphosphocholine micelles was studied by nuclear magnetic resonance spectroscopy. The set of 20 structures obtained has a bent helical conformation with a mean backbone root mean square deviation value of approximately 0.2 A and resembles the structure in isotropic solvents (Balashova et al., 2000. NMR structure of the channel-former zervamicin IIB in isotropic solvents. FEBS Lett 466:333-336). The N-terminus represents an alpha-helix, whereas the C-terminal part has a mixed 3(10)/alpha(R) hydrogen-bond pattern. In the anisotropic micelle environment, the bending angle on Hyp10 (23 degrees) is smaller than that (47 degrees) in isotropic solvents. In the NOESY (Nuclear Overhauser Effect Spectroscopy) spectra, the characteristic attenuation of the peptide signals by 5- and 16-doxylstearate relaxation probes indicates a peripheral mode of the peptaibol binding to the micelle with the N-terminus immersed slightly deeper into micelle interior. Analysis of the surface hydrophobicity reveals that the zervamicin IIB helix is amphiphilic and well suited to formation of a tetrameric transmembrane bundle, according to the barrel-stave mechanism. The results are discussed in a context of voltage-driven peptaibol insertion into membrane.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19720036 C.K.Wang, M.L.Colgrave, D.C.Ireland, Q.Kaas, and D.J.Craik (2009).
Despite a conserved cystine knot motif, different cyclotides have different membrane binding modes.
  Biophys J, 97, 1471-1481.
PDB codes: 2kcg 2kch
19211551 C.K.Wang, S.H.Hu, J.L.Martin, T.Sjögren, J.Hajdu, L.Bohlin, P.Claeson, U.Göransson, K.J.Rosengren, J.Tang, N.H.Tan, and D.J.Craik (2009).
Combined X-ray and NMR Analysis of the Stability of the Cyclotide Cystine Knot Fold That Underpins Its Insecticidal Activity and Potential Use as a Drug Scaffold.
  J Biol Chem, 284, 10672-10683.
PDB codes: 2k7g 3e4h
19708686 D.N.Langelaan, and J.K.Rainey (2009).
Headgroup-dependent membrane catalysis of apelin-receptor interactions is likely.
  J Phys Chem B, 113, 10465-10471.  
18835909 E.S.Salnikov, H.Friedrich, X.Li, P.Bertani, S.Reissmann, C.Hertweck, J.D.O'Neil, J.Raap, and B.Bechinger (2009).
Structure and alignment of the membrane-associated peptaibols ampullosporin A and alamethicin by oriented 15N and 31P solid-state NMR spectroscopy.
  Biophys J, 96, 86.  
17589863 A.D.Milov, Y.D.Tsvetkov, E.Y.Gorbunova, L.G.Mustaeva, T.V.Ovchinnikova, J.W.Handgraaf, and J.Raap (2007).
Solvent effects on the secondary structure of the membrane-active zervamicin determined by PELDOR spectroscopy.
  Chem Biodivers, 4, 1243-1255.  
17695323 T.V.Ovchinnikova, and A.N.Murashev (2007).
The peptaibol antibiotic zervamicin displays neurotropic activity.
  Dokl Biochem Biophys, 414, 146-148.  
17589870 T.V.Ovchinnikova, N.G.Levitskaya, O.G.Voskresenskaya, Z.A.Yakimenko, A.A.Tagaev, A.Y.Ovchinnikova, A.N.Murashev, and A.A.Kamenskii (2007).
Neuroleptic properties of the ion-channel-forming peptaibol zervamicin: locomotor activity and behavioral effects.
  Chem Biodivers, 4, 1374-1387.  
17589862 Z.O.Shenkarev, A.S.Paramonov, K.D.Nadezhdin, E.V.Bocharov, I.A.Kudelina, D.A.Skladnev, A.A.Tagaev, Z.A.Yakimenko, T.V.Ovchinnikova, and A.S.Arseniev (2007).
Antiamoebin I in methanol solution: rapid exchange between right-handed and left-handed 3(10)-helical conformations.
  Chem Biodivers, 4, 1219-1242.  
17215879 J.K.Rainey, L.Fliegel, and B.D.Sykes (2006).
Strategies for dealing with conformational sampling in structural calculations of flexible or kinked transmembrane peptides.
  Biochem Cell Biol, 84, 918-929.  
16937243 J.Raap, J.Hollander, T.V.Ovchinnikova, N.V.Swischeva, D.Skladnev, and S.Kiihne (2006).
Trans and surface membrane bound zervamicin IIB: 13C-MAOSS-NMR at high spinning speed.
  J Biomol NMR, 35, 285-293.  
16817894 Z.O.Shenkarev, K.D.Nadezhdin, V.A.Sobol, A.G.Sobol, L.Skjeldal, and A.S.Arseniev (2006).
Conformation and mode of membrane interaction in cyclotides. Spatial structure of kalata B1 bound to a dodecylphosphocholine micelle.
  FEBS J, 273, 2658-2672.
PDB code: 1znu
15635654 J.Raap, K.Erkelens, A.Ogrel, D.A.Skladnev, and H.Brückner (2005).
Fungal biosynthesis of non-ribosomal peptide antibiotics and alpha, alpha-dialkylated amino acid constituents.
  J Pept Sci, 11, 331-338.  
16331966 R.Brunecky, S.Lee, P.W.Rzepecki, M.Overduin, G.D.Prestwich, A.G.Kutateladze, and T.G.Kutateladze (2005).
Investigation of the binding geometry of a peripheral membrane protein.
  Biochemistry, 44, 16064-16071.  
15189865 Z.O.Shenkarev, T.A.Balashova, Z.A.Yakimenko, T.V.Ovchinnikova, and A.S.Arseniev (2004).
Peptaibol zervamicin IIb structure and dynamics refinement from transhydrogen bond J couplings.
  Biophys J, 86, 3687-3699.
PDB code: 1r9u
14658793 G.Bunkóczi, M.Schiell, L.Vértesy, and G.M.Sheldrick (2003).
Crystal structures of cephaibols.
  J Pept Sci, 9, 745-752.
PDB codes: 1ob4 1ob6 1ob7
14658792 M.Kronen, H.Görls, H.H.Nguyen, S.Reissmann, M.Bohl, J.Sühnel, and U.Gräfe (2003).
Crystal structure and conformational analysis of ampullosporin A.
  J Pept Sci, 9, 729-744.  
12524274 T.P.Galbraith, R.Harris, P.C.Driscoll, and B.A.Wallace (2003).
Solution NMR studies of antiamoebin, a membrane channel-forming polypeptide.
  Biophys J, 84, 185-194.
PDB code: 1gq0
14658801 T.V.Ovchinnikova, Z.O.Shenkarev, Z.A.Yakimenko, N.V.Svishcheva, A.A.Tagaev, D.A.Skladnev, and A.S.Arseniev (2003).
Biosynthetic uniform 13C,15N-labelling of zervamicin IIB. Complete 13C and 15N NMR assignment.
  J Pept Sci, 9, 817-826.
PDB code: 1r9u
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.