3SBN

trichovirin I-4A in polar environment at 0.9 Angstroem

• PDB DOI: https://doi.org/10.2210/pdb3SBN/pdb

• Classification: ANTIBIOTIC
• Organism(s): Trichoderma viride
• Mutation(s): No 


• Deposited: 2011-06-06 Released: 2011-12-28 
• Deposition Author(s): Gessmann, R., Axford, D., Petratos, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free: 0.128 
• R-Value Observed: 0.102 

Literature

Four complete turns of a curved 310-helix at atomic resolution: The crystal structure of the peptaibol trichovirin I-4A in polar environment suggests a transition to alpha-helix for membrane function

Gessmann, R., Axford, D., Owen, R.L., Bruckner, H., Petratos, K.

(2012) Acta Crystallogr D Biol Crystallogr 68: 109-116

• PubMed: 22281739 
• DOI: https://doi.org/10.1107/S090744491105133X
• Primary Citation of Related Structures:  
  3SBN


• PubMed Abstract: 
  

  The first crystal structure of a member of peptaibol antibiotic subfamily 4, trichovirin I-4A (14 residues), has been determined by direct methods and refined at atomic resolution. The monoclinic unit cell has two molecules in the asymmetric unit. Both molecules assume a 3₁₀ right-handed helical conformation and are significantly bent. The molecules pack loosely along the crystallographic twofold axis, forming two large tunnels between symmetry-related molecules in which no ordered solvent could be located. Carbonyl O atoms which are not involved in intramolecular hydrogen bonding participate in close van der Waals interactions with apolar groups. The necessary amphipathicity for biological activity of peptaibols is not realised in the crystal structure. Hence, a structural change of trichovirin to an α-helical conformation is proposed for membrane integration and efficient water/ion transportation across the lipid bilayer.

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Organizational Affiliation: 

IMBB-FORTH, N. Plastira 100, Heraklion, Crete 70013, Greece.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 2.89 kDa 
• Atom Count: 236 
• Modelled Residue Count: 30 
• Deposited Residue Count: 30 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trichovirin I-4A	A, B	15	Trichoderma viride	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CCN	C [auth A], D [auth A]	ACETONITRILE C2 H3 N WEVYAHXRMPXWCK-UHFFFAOYSA-N
MOH	E [auth B], F [auth B]	METHANOL C H4 O OKKJLVBELUTLKV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB	A, B	L-PEPTIDE LINKING	C4 H9 N O2		ALA

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000828	A, B	Trichovirin I-4A	Peptaibol / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free: 0.128 
• R-Value Observed: 0.102 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.284	α = 90
b = 9.896	β = 97.15
c = 37.567	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
ACORN	phasing
SHELXL	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Gessmann, R., Axford, D., Petratos, K.

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2012-02-15
  Changes: Database references
• Version 1.2: 2012-12-12
  Changes: Other
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations