Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 12088.70 
• Atom Count: 830 
• 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

• DOI: 10.2210/pdb3KQ6/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Mutation(s): 2 


• 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: 1.9 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


• 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: 

• 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
• 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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Insulin A chain	A, C	21	Homo sapiens	Mutation(s): 2  Gene Names: INS
Find proteins for P01308 (Homo sapiens) Go to Gene View: INS Go to UniProtKB:  P01308

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Insulin B chain	B, D	30	Homo sapiens	Mutation(s): 0  Gene Names: INS
Find proteins for P01308 (Homo sapiens) Go to Gene View: INS Go to UniProtKB:  P01308

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	A, D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
IPH	C	PHENOL C6 H6 O ISWSIDIOOBJBQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.257 
• R-Value Work: 0.199 
• Space Group: H 3

Unit Cell:

Length (Å)	Angle (°)
a = 78.091	α = 90.00
b = 78.091	β = 90.00
c = 36.399	γ = 120.00

Software Package:

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

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
  Type: Version format compliance