Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 276.11 kDa 
• Atom Count: 19098 
• Modelled Residue Count: 2348 
• Deposited Residue Count: 2502 
• Unique protein chains: 1

4PPH

Crystal structure of conglutin gamma, a unique basic 7S globulin from lupine seeds

• PDB DOI: 10.2210/pdb4PPH/pdb

• Classification: PLANT PROTEIN
• Organism(s): Lupinus angustifolius
• Mutation(s): No 


• Deposited: 2014-02-27 Released: 2015-02-11 
• Deposition Author(s): Czubinski, J., Barciszewski, J., Gilski, M., Lampart-Szczapa, E., Jaskolski, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.174 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 

Literature

Structure of gamma-conglutin: insight into the quaternary structure of 7S basic globulins from legumes.

Czubinski, J., Barciszewski, J., Gilski, M., Szpotkowski, K., Debski, J., Lampart-Szczapa, E., Jaskolski, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 224-238

• PubMed: 25664733 
• DOI: 10.1107/S1399004714025073
• Primary Citation of Related Structures:  
  4PPH


• PubMed Abstract: 
  

γ-Conglutin from lupin seeds is an unusual 7S basic globulin protein. It is capable of reducing glycaemia in mammals, but the structural basis of this activity is not known. γ-Conglutin shares a high level of structural homology with glycoside hydrolase inhibitor proteins, although it lacks any kind of inhibitory activity against plant cell-wall degradation enzymes. In addition, γ-conglutin displays a less pronounced structural similarity to pepsin-like aspartic proteases, but it is proteolytically dysfunctional. Only one structural study of a legume 7S basic globulin, that isolated from soybean, has been reported to date. The quaternary assembly of soybean 7S basic globulin (Bg7S) is arranged as a cruciform-shaped tetramer comprised of two superposed dimers. Here, the crystal structure of γ-conglutin isolated from Lupinus angustifolius seeds (LangC) is presented. The polypeptide chain of LangC is post-translationally cleaved into α and β subunits but retains its covalent integrity owing to a disulfide bridge. The protomers of LangC undergo an intricate quaternary assembly, resulting in a ring-like hexamer with noncrystallographic D3 symmetry. The twofold-related dimers are similar to those in Bg7S but their assembly is different as a consequence of mutations in a β-strand that is involved in intermolecular β-sheet formation in γ-conglutin. Structural elucidation of γ-conglutin will help to explain its physiological role, especially in the evolutionary context, and will guide further research into the hypoglycaemic activity of this protein in humans, with potential consequences for novel antidiabetic therapies.

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Related Citations: 

• Characterisation of different digestion susceptibility of lupin seed globulins.
  Czubinski, J., Dwiecki, K., Siger, A., Neunert, G., Lampart-Szczapa, E.
  (2014) Food Chem 143: 418

• Release of flavonoids from lupin globulin proteins during digestion in a model system.
  Czubinski, J., Dwiecki, K., Siger, A., Kachlicki, P., Neunert, G., Lampart-Szczapa, E., Nogala-Kalucka, M.
  (2012) J Agric Food Chem 60: 1830

• Crystal structure of basic 7S globulin, a xyloglucan-specific endo-beta-1,4-glucanase inhibitor protein-like protein from soybean lacking inhibitory activity against endo-beta-glucanase.
  Yoshizawa, T., Shimizu, T., Yamabe, M., Taichi, M., Nishiuchi, Y., Shichijo, N., Unzai, S., Hirano, H., Sato, M., Hashimoto, H.
  (2011) FEBS J 278: 1944

• Internalisation and multiple phosphorylation of gamma-Conglutin, the lupin seed glycaemia-lowering protein, in HepG2 cells.
  Capraro, J., Magni, C., Faoro, F., Maffi, D., Scarafoni, A., Tedeschi, G., Maffioli, E., Parolari, A., Manzoni, C., Lovati, M.R., Duranti, M.
  (2013) Biochem Biophys Res Commun 437: 648

• Lupin seed gamma-conglutin lowers blood glucose in hyperglycaemic rats and increases glucose consumption of HepG2 cells.
  Lovati, M.R., Manzoni, C., Castiglioni, S., Parolari, A., Magni, C., Duranti, M.
  (2012) Br J Nutr 107: 67

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Organizational Affiliation: 

Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conglutin gamma	A, B, C, D, E, F	417	Lupinus angustifolius	Mutation(s): 0  Gene Names: LOC109345795, TanjilG_29300
UniProt
Find proteins for Q42369 (Lupinus angustifolius) Explore Q42369  Go to UniProtKB:  Q42369

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	G	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G11971MR GlyCosmos:  G11971MR GlyGen:  G11971MR

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	H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth D], O [auth B], U [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth E], L [auth A], LA [auth F], M [auth A], MA [auth F], N [auth A], NA [auth F], OA [auth F], P [auth B], PA [auth F], Q [auth B], QA [auth F], R [auth B], S [auth B], T [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.174 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.99	α = 90
b = 121.99	β = 90
c = 188.49	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-02-27 
• Released Date: 2015-02-11 
Deposition Author(s): Czubinski, J., Barciszewski, J., Gilski, M., Lampart-Szczapa, E., Jaskolski, M.

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Advisory, Database references, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary