Biological Assembly 1  

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

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

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

Macromolecule Content

• Total Structure Weight: 12.09 kDa 
• Atom Count: 912 
• Modelled Residue Count: 102 
• Deposited Residue Count: 102 
• Unique protein chains: 2

3KQ6

Enhancing the Therapeutic Properties of a Protein by a Designed Zinc-Binding Site, Structural principles of a novel long-acting insulin analog

• PDB DOI: 10.2210/pdb3KQ6/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2009-11-17 Released: 2010-02-23 
• Deposition Author(s): Wan, Z.L., Hu, S.Q., Whittaker, L., Phillips, N.B., Whittake, J., Ismail-Beigi, F., Weiss, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.257 
• R-Value Work: 0.199 

Literature

Supramolecular protein engineering: design of zinc-stapled insulin hexamers as a long acting depot.

Phillips, N.B., Wan, Z.L., Whittaker, L., Hu, S.Q., Huang, K., Hua, Q.X., Whittaker, J., Ismail-Beigi, F., Weiss, M.A.

(2010) J Biol Chem 285: 11755-11759

• PubMed: 20181952 
• DOI: 10.1074/jbc.C110.105825
• Primary Citation of Related Structures:  
  3KQ6


• PubMed Abstract: 
  

Bottom-up control of supramolecular protein assembly can provide a therapeutic nanobiotechnology. We demonstrate that the pharmacological properties of insulin can be enhanced by design of "zinc staples" between hexamers. Paired (i, i+4) His substitutions were introduced at an alpha-helical surface. The crystal structure contains both classical axial zinc ions and novel zinc ions at hexamer-hexamer interfaces. Although soluble at pH 4, the combined electrostatic effects of the substitutions and bridging zinc ions cause isoelectric precipitation at neutral pH. Following subcutaneous injection in a diabetic rat, the analog effected glycemic control with a time course similar to that of long acting formulation Lantus. Relative to Lantus, however, the analog discriminates at least 30-fold more stringently between the insulin receptor and mitogenic insulin-like growth factor receptor. Because aberrant mitogenic signaling may be associated with elevated cancer risk, such enhanced specificity may improve safety. Zinc stapling provides a general strategy to modify the pharmacokinetic and biological properties of a subcutaneous protein depot.

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Related Citations: 

• Enhancing the activity of insulin at the receptor interface: crystal structure and photo-cross-linking of A8 analogues.
  Wan, Z.L., Xu, B., Chu, Y.C., Li, B., Nakagawa, S.H., Qu, Y., Hu, S.Q., Katsoyannis, P.G., Weiss, M.A.
  (2004) Biochemistry 43: 16119

• The structure of 2zn pig insulin crystal at 1.5 A resolution
  Baker, E.N., Blundell, T.L., Cutfield, J.F., Cutfield, S.M., Dodson, E.J., Dodson, G.G., Hodgkin, D., Isaacs, N.W., Reynolds, C.D.
  (1988) Philos Trans R Soc London,ser B 319: 369

• Structure of insulin in 4-zinc insulin
  Bentley, G., Dodson, E., Dodson, G., Hodgkin, D., Mercola, D.
  (1976) Nature 261: 166

• Phenol stabilizes more helix in a new symmetrical zinc insulin hexamer
  Derewenda, U., Derewenda, Z., Dodson, E., Dodson, G., Reynold, C., Smith, G., Sparks, C., Swenson, D.
  (1989) Nature 338: 594

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Organizational Affiliation: 

Department of Biochemistry, Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin A chain	A, C	21	Homo sapiens	Mutation(s): 2  Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin B chain	B, D	30	Homo sapiens	Mutation(s): 0  Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPH	H [auth C]	PHENOL C6 H6 O ISWSIDIOOBJBQZ-UHFFFAOYSA-N
ZN	E [auth A], G [auth B], I [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A], J [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.257 
• R-Value Work: 0.199 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.091	α = 90
b = 78.091	β = 90
c = 36.399	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-11-17 
• Released Date: 2010-02-23 
Deposition Author(s): Wan, Z.L., Hu, S.Q., Whittaker, L., Phillips, N.B., Whittake, J., Ismail-Beigi, F., Weiss, M.A.

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations