2R36 | pdb_00002r36

Crystal structure of ni human ARG-insulin

• PDB DOI: https://doi.org/10.2210/pdb2R36/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-08-29 Released: 2008-09-02 
• Deposition Author(s): Sreekanth, R., Pattabhi, V., Rajan, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.255 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.300 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Metal induced structural changes observed in hexameric insulin

Sreekanth, R., Pattabhi, V., Rajan, S.S.

(2009) Int J Biol Macromol 44: 29-36

• PubMed: 18977386 
• DOI: https://doi.org/10.1016/j.ijbiomac.2008.09.019
• Primary Citation of Related Structures:  
  2R34, 2R35, 2R36


• PubMed Abstract: 
  

  The metal ions in insulin hexamer play a crucial role in the T to R conformational transitions. We have determined the crystal structures of 2Mn2+, 1Rb1+ and 4Ni2+ human arg-insulin and compared them with the 2Zn2+ structure. The first two structures exist in the T3R3f state like the native 2Zn2+ arg-insulin, while the 4Ni2+ adopts a T6 conformation. The metal coordination is found to be tetrahedral in all the structures except that of nickel where a dual octahedral and tetrahedral coordination is found at one site. Rubidium occupies only one of the high affinity metal binding sites. The metal induced structural changes observed, have been explained.

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Organizational Affiliation: 
• Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 12.24 kDa 
• Atom Count: 881 
• Modeled Residue Count: 104 
• Deposited Residue Count: 104 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin	A, C	22	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308 GTEx:  ENSG00000254647

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin	B, D	30	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308
PHAROS:  P01308 GTEx:  ENSG00000254647

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	E [auth B], F [auth B], G [auth D], H [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	J [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	I [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.255 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.300 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.953	α = 90
b = 83.953	β = 90
c = 40.222	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
AUTOMAR	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Sreekanth, R., Pattabhi, V., Rajan, S.S.

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary