5V3S | pdb_00005v3s

Crystal structure of IP-1A from Alcaligenes faecalis at 1.8A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.270 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

An Alcaligenes strain emulates Bacillus thuringiensis producing a binary protein that kills corn rootworm through a mechanism similar to Cry34Ab1/Cry35Ab1.

Yalpani, N.Altier, D.Barry, J.Kassa, A.Nowatzki, T.M.Sethi, A.Zhao, J.Z.Diehn, S.Crane, V.Sandahl, G.Guan, R.Poland, B.Perez Ortega, C.Nelson, M.E.Xie, W.Liu, L.Wu, G.

(2017) Sci Rep 7: 3063-3063

  • DOI: https://doi.org/10.1038/s41598-017-03544-9

  • PubMed Abstract: 

    Crops expressing Bacillus thuringiensis (Bt)-derived insecticidal protein genes have been commercially available for over 15 years and are providing significant value to growers. However, there remains the need for alternative insecticidal actives due to emerging insect resistance to certain Bt proteins. A screen of bacterial strains led to the discovery of a two-component insecticidal protein named AfIP-1A/1B from an Alcaligenes faecalis strain. This protein shows selectivity against coleopteran insects including western corn rootworm (WCR). Transgenic maize plants expressing AfIP-1A/1B demonstrate strong protection from rootworm injury. Surprisingly, although little sequence similarity exists to known insecticidal proteins, efficacy tests using WCR populations resistant to two different Cry proteins show that AfIP-1A/1B and mCry3A differ in their mode of action while AfIP-1A/1B and the binary Cry34Ab1/Cry35Ab1 protein share a similar mode. These findings are supported by results of competitive binding assays and the similarity of the x-ray structure of AfIP-1A to Cry34Ab1. Our work indicates that insecticidal proteins obtained from a non-Bt bacterial source can be useful for developing genetically modified crops and can function similarly to familiar proteins from Bt.


  • Organizational Affiliation
    • DuPont Pioneer, Johnston, IA, 50131, USA. nasser.yalpani@pioneer.com.

Macromolecule Content 

  • Total Structure Weight: 34.75 kDa 
  • Atom Count: 2,525 
  • Modeled Residue Count: 286 
  • Deposited Residue Count: 308 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Two-component insecticidal protein 16 kDa unit
A, B
154Alcaligenes faecalisMutation(s): 0 
Gene Names: IP-1A
UniProt
Find proteins for A0A0U4HUZ5 (Alcaligenes faecalis)
Explore A0A0U4HUZ5 
Go to UniProtKB:  A0A0U4HUZ5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U4HUZ5
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.270 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.288α = 90
b = 34.419β = 96.54
c = 71.436γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CRANKphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary