Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 24.66 kDa 
• Atom Count: 2166 
• Residue Count: 222 
• Unique protein chains: 1

6EIO

Crystal structure of an ice binding protein from an Antarctic Biological Consortium

• DOI: 10.2210/pdb6EIO/pdb

• Classification: ANTIFREEZE PROTEIN
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-19 Released: 2018-03-28 
• Deposition Author(s): Nardini, M., Mangiagalli, M., Nardone, V., Bar Dolev, M., Vena, V.F., Sarusi, G., Braslavsky, I., Lotti, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.84 Å
• R-Value Free: 0.128 
• R-Value Work: 0.115 
• R-Value Observed: 0.116 

Literature

Structure of a bacterial ice binding protein with two faces of interaction with ice.

Mangiagalli, M., Sarusi, G., Kaleda, A., Bar Dolev, M., Nardone, V., Vena, V.F., Braslavsky, I., Lotti, M., Nardini, M.

(2018) FEBS J 285: 1653-1666

• PubMed: 29533528 
• DOI: 10.1111/febs.14434
• Primary Citation of Related Structures:  
  6EIO


• PubMed Abstract: 
  

Ice-binding proteins (IBPs) contribute to the survival of many living beings at subzero temperature by controlling the formation and growth of ice crystals. This work investigates the structural basis of the ice-binding properties of EfcIBP, obtained from Antarctic bacteria. EfcIBP is endowed with a unique combination of thermal hysteresis and ice recrystallization inhibition activity. The three-dimensional structure, solved at 0.84 Å resolution, shows that EfcIBP belongs to the IBP-1 fold family, and is organized in a right-handed β-solenoid with a triangular cross-section that forms three protein surfaces, named A, B, and C faces. However, EfcIBP diverges from other IBP-1 fold proteins in relevant structural features including the lack of a 'capping' region on top of the β-solenoid, and in the sequence and organization of the regions exposed to ice that, in EfcIBP, reveal the presence of threonine-rich ice-binding motifs. Docking experiments and site-directed mutagenesis pinpoint that EfcIBP binds ice crystals not only via its B face, as common to other IBPs, but also via ice-binding sites on the C face.

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Organizational Affiliation: 

Department of Biosciences, University of Milano, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antifreeze protein	A	237	uncultured bacterium	Mutation(s): 0
Find proteins for A0A023J6X7 (uncultured bacterium) Explore A0A023J6X7  Go to UniProtKB:  A0A023J6X7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.84 Å
• R-Value Free: 0.128 
• R-Value Work: 0.115 
• R-Value Observed: 0.116 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.482	α = 90
b = 50.717	β = 90
c = 92.452	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-09-19 
• Released Date: 2018-03-28 
Deposition Author(s): Nardini, M., Mangiagalli, M., Nardone, V., Bar Dolev, M., Vena, V.F., Sarusi, G., Braslavsky, I., Lotti, M.

Revision History 

• Version 1.0: 2018-03-28
  Type: Initial release
  
• Version 1.1: 2018-04-25
  Changes: Data collection, Database references
• Version 1.2: 2018-05-16
  Changes: Data collection, Database references