Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 21.62 kDa 
• Atom Count: 1655 
• Residue Count: 251 
• Unique protein chains: 1

7JJV

Crystal waters on the nine polyproline type II helical bundle springtail antifreeze protein from Granisotoma rainieri match the ice lattice

• DOI: 10.2210/pdb7JJV/pdb

• Classification: ANTIFREEZE PROTEIN
• Organism(s): unclassified Entomobryomorpha
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-07-27 Released: 2021-01-27 
• Deposition Author(s): Scholl, C.L., Tsuda, S., Graham, L.A., Davies, P.L.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.180 
• R-Value Work: 0.149 

Literature

Crystal waters on the nine polyproline type II helical bundle springtail antifreeze protein from Granisotoma rainieri match the ice lattice.

Scholl, C.L., Tsuda, S., Graham, L.A., Davies, P.L.

(2021) FEBS J 

• PubMed: 33460499 
• DOI: 10.1111/febs.15717
• Primary Citation of Related Structures:  
  7JJV


• PubMed Abstract: 
  

A springtail (Collembola) identified as Granisotoma rainieri was collected from snow in Hokkaido, Japan in late winter when nighttime temperatures were below zero. Extracts of these arthropods showed antifreeze activity by shaping ice crystals and stopping their growth. The glycine-rich proteins responsible for this freezing point depression were isolated by ice-affinity purification and had principal masses of ~6.9 and 9.6 kDa. We identified a transcript for a 9.6-kDa component and produced it as a His-tagged recombinant protein for structural analysis. Its crystal structure was solved to a resolution of 1.21 Å and revealed a polyproline type II helical bundle, similar to the six-helix Hypogastrura harveyi AFP, but with nine helices organized into two layers held together by an extensive network of hydrogen bonds. One of the layers is flat, regular, and hydrophobic and likely serves as the ice-binding side. Although this surface makes close protein-protein contacts with its symmetry mate in the crystal, it has bound chains of waters present that resemble those on the basal and primary prisms planes of ice. Molecular dynamics simulations indicate most of these crystal waters would preferentially occupy these sites if exposed to bulk solvent in the absence of the symmetry mate. These pre-positioned waters lend further support to the ice-binding mechanism in which AFPs organize ice-like waters on one surface to adsorb to ice.

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Organizational Affiliation: 

Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GrAFP antifreeze protein	A, B	132	unclassified Entomobryomorpha	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.180 
• R-Value Work: 0.149 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.489	α = 90
b = 64.214	β = 90
c = 86.267	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-07-27 
• Released Date: 2021-01-27 
Deposition Author(s): Scholl, C.L., Tsuda, S., Graham, L.A., Davies, P.L.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History 

• Version 1.0: 2021-01-27
  Type: Initial release