Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 1.82 kDa 
• Atom Count: 131 
• Modelled Residue Count: 17 
• Deposited Residue Count: 17 
• Unique protein chains: 1

1IH9

NMR Structure of Zervamicin IIB (peptaibol antibiotic) Bound to DPC Micelles

• PDB DOI: 10.2210/pdb1IH9/pdb
• BMRB: 4993

• Classification: ANTIBIOTIC
• Organism(s): Emericellopsis salmosynnemata
• Mutation(s): No 


• Deposited: 2001-04-19 Released: 2002-02-13 
• Deposition Author(s): Shenkarev, Z.O., Balasheva, T.A., Efremov, R.G., Yakimenko, Z.A., Ovchinnikova, T.V., Raap, J., Arseniev, A.S.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Spatial Structure of Zervamicin Iib Bound to Dpc Micelles: Implications for Voltage-Gating.

Shenkarev, Z.O., Balashova, T.A., Efremov, R.G., Yakimenko, Z.A., Ovchinnikova, T.V., Raap, J., Arseniev, A.S.

(2002) Biophys J 82: 762

• PubMed: 11806918 
• DOI: 10.1016/S0006-3495(02)75438-6
• Primary Citation of Related Structures:  
  1IH9


• PubMed Abstract: 
  

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.

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Organizational Affiliation: 

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZERVAMICIN IIB	A	17	Emericellopsis salmosynnemata	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB	A	L-PEPTIDE LINKING	C4 H9 N O2		ALA
HYP	A	L-PEPTIDE LINKING	C5 H9 N O3		PRO
PHL	A	L-PEPTIDE LINKING	C9 H13 N O		PHE

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000159	A	Zervamicin IIB	Peptaibol / Antibiotic		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 
• OLDERADO: 1IH9 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-04-19 
• Released Date: 2002-02-13 
Deposition Author(s): Shenkarev, Z.O., Balasheva, T.A., Efremov, R.G., Yakimenko, Z.A., Ovchinnikova, T.V., Raap, J., Arseniev, A.S.

Revision History  

• Version 1.0: 2002-02-13
  Type: Initial release
  
• Version 1.1: 2011-06-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-07-27
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 1.4: 2012-12-12
  Changes: Other