2ZPP | pdb_00002zpp

Neutron crystal structure of cubic insulin at pD9

• PDB DOI: https://doi.org/10.2210/pdb2ZPP/pdb

• Classification: HORMONE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2008-07-26 Released: 2008-10-28 
• Deposition Author(s): Ishikawa, T., Tanaka, I., Niimura, N.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.260 (Depositor) 
• R-Value Work: 
  0.221 (Depositor) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

An abnormal pK(a) value of internal histidine of the insulin molecule revealed by neutron crystallographic analysis

Ishikawa, T., Chatake, T., Morimoto, Y., Maeda, M., Kurihara, K., Tanaka, I., Niimura, N.

(2008) Biochem Biophys Res Commun 376: 32-35

• PubMed: 18725203 
• DOI: https://doi.org/10.1016/j.bbrc.2008.08.071
• Primary Citation Related Structures: 
  2ZPP


• PubMed Abstract: 
  

  Insulin is stored in pancreatic beta-cell as hexameric form with Zn2+ ions, while the hormonally active form is monomer. The hexamer requires the coordination of Zn2+ ions to the HisB10. In order to reveal the mechanism of the hexamerization of insulin, we investigated the Zn2+ free insulin at pD6.6 and pD9 by neutron crystallographic analyses. HisB10 is doubly protonated not only at pD6.6 but also at pD9, indicating an abnormal pK(a) of this histidine. It is suggested that HisB10 acts on a strong cation capture and contributes to the high stability of the hexameric form in pancreas.

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Organizational Affiliation: 
• Kyoto University Research Reactor, Asashironishi 2, Kumatori, Osaka 590-0494, Japan.

Biological Assembly 1  

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: 5.79 kDa 
• Atom Count: 437 
• Modeled Residue Count: 51 
• Deposited Residue Count: 51 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin A chain	A	21	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P01315 (Sus scrofa) Explore P01315  Go to UniProtKB:  P01315

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin B chain	B	30	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P01315 (Sus scrofa) Explore P01315  Go to UniProtKB:  P01315

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.260 (Depositor) 
• R-Value Work:  0.221 (Depositor) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.04	α = 90
b = 79.04	β = 90
c = 79.04	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Ishikawa, T., Tanaka, I., Niimura, N.

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2013-08-21
  Changes: Other
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-23
  Changes: Structure summary