1C3M

CRYSTAL STRUCTURE OF HELTUBA COMPLEXED TO MAN(1-3)MAN

• PDB DOI: https://doi.org/10.2210/pdb1C3M/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Helianthus tuberosus
• Mutation(s): No 


• Deposited: 1999-07-28 Released: 2000-01-10 
• Deposition Author(s): Bourne, Y., Zamboni, V., Barre, A., Peumans, W.J., van Damme, E.J.M., Rouge, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.217 
• R-Value Work: 0.171 

Literature

Helianthus tuberosus lectin reveals a widespread scaffold for mannose-binding lectins.

Bourne, Y., Zamboni, V., Barre, A., Peumans, W.J., Van Damme, E.J., Rouge, P.

(1999) Structure 7: 1473-1482

• PubMed: 10647178 
• DOI: https://doi.org/10.1016/s0969-2126(00)88338-0
• Primary Citation of Related Structures:  
  1C3K, 1C3M, 1C3N


• PubMed Abstract: 
  

  Heltuba, a tuber lectin from the Jerusalem artichoke Helianthus tuberosus, belongs to the mannose-binding subgroup of the family of jacalin-related plant lectins. Heltuba is highly specific for the disaccharides Man alpha 1-3Man or Man alpha 1-2Man, two carbohydrates that are particularly abundant in the glycoconjugates exposed on the surface of viruses, bacteria and fungi, and on the epithelial cells along the gastrointestinal tract of lower animals. Heltuba is therefore a good candidate as a defense protein against plant pathogens or predators.

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Organizational Affiliation: 

AFMB-CNRS, Marseille, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.84 kDa 
• Atom Count: 1,164 
• Modelled Residue Count: 145 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AGGLUTININ	A	147	Helianthus tuberosus	Mutation(s): 0
UniProt
Find proteins for Q9ZQY5 (Helianthus tuberosus) Explore Q9ZQY5  Go to UniProtKB:  Q9ZQY5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G00891MP GlyCosmos:  G00891MP GlyGen:  G00891MP

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900112	B	3alpha-alpha-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.217 
• R-Value Work: 0.171 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.373	α = 90
b = 106.373	β = 90
c = 65.099	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-10 
Deposition Author(s): Bourne, Y., Zamboni, V., Barre, A., Peumans, W.J., van Damme, E.J.M., Rouge, P.

Revision History  

• Version 1.0: 2000-01-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-02-07
  Changes: Data collection, Database references, Structure summary