Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 59.30 kDa 
• Atom Count: 4413 
• Modelled Residue Count: 510 
• Deposited Residue Count: 517 
• Unique protein chains: 2

3O5W

Binding of kinetin in the active site of mistletoe lectin I

• DOI: 10.2210/pdb3O5W/pdb

• Classification: HYDROLASE
• Organism(s): Viscum album
• Mutation(s): No 


• Deposited: 2010-07-28 Released: 2011-09-14 
• Deposition Author(s): Malecki, P.H., Meyer, A., Rypniewski, W., Szymanski, M., Barciszewski, J., Betzel, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.226 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 

Literature

Binding of the plant hormone kinetin in the active site of Mistletoe Lectin I from Viscum album.

Malecki, P.H., Rypniewski, W., Szymanski, M., Barciszewski, J., Meyer, A.

(2012) Biochim Biophys Acta 1824: 334-338

• PubMed: 22064121 
• DOI: 10.1016/j.bbapap.2011.10.013
• Primary Citation of Related Structures:  
  3O5W


• PubMed Abstract: 
  

The crystal structure of the ribosome inhibiting protein Mistletoe Lectin I (ML-I) derived from the European mistletoe, Viscum album, in complex with kinetin has been refined at 2.7Å resolution. Suitably large crystals of ML-I were obtained applying the counter diffusion method using the Gel Tube R Crystallization Kit (GT-R) on board the Russian Service Module on the international space station ISS within the GCF mission No. 6, arranged by the Japanese aerospace exploration agency (JAXA). Hexagonal bi-pyramidal crystals were grown during three months under microgravity. Before data collection the crystals were soaked in a saturated solution of kinetin and diffraction data to 2.7Å were collected using synchrotron radiation and cryogenic techniques. The atomic model was refined and revealed a single kinetin molecule in the ribosome inactivation site of ML-I. The complex demonstrates the feasibility of mistletoe to bind plant hormones out of the host regulation system as part of a self protection mechanism.

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Organizational Affiliation: 

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactoside-specific lectin 1 chain A isoform 1	A	254	Viscum album	Mutation(s): 0  EC: 3.2.2.22
Find proteins for P81446 (Viscum album) Explore P81446  Go to UniProtKB:  P81446

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactoside-specific lectin 1 chain B	B	263	Viscum album	Mutation(s): 0  EC: 3.2.2.22
Find proteins for P81446 (Viscum album) Explore P81446  Go to UniProtKB:  P81446

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	2		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
H35	A	N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE C10 H9 N5 O QANMHLXAZMSUEX-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	D	triacetyl-beta-chitotriose	Oligosaccharide /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.226 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.573	α = 90
b = 107.573	β = 90
c = 310.633	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-28 
• Released Date: 2011-09-14 
Deposition Author(s): Malecki, P.H., Meyer, A., Rypniewski, W., Szymanski, M., Barciszewski, J., Betzel, C.

Revision History  

• Version 1.0: 2011-09-14
  Type: Initial release
  
• Version 1.1: 2012-10-10
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Structure summary