1G7A

1.2 A structure of T3R3 human insulin at 100 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Phase changes in T(3)R(3)(f) human insulin: temperature or pressure induced?

Smith, G.D.Pangborn, W.A.Blessing, R.H.

(2001) Acta Crystallogr.,Sect.D 57: 1091-1100

  • Primary Citation of Related Structures:  1G7B

  • PubMed Abstract: 
  • The structure of T(3)R(3) hexameric human insulin has been determined at 100 K from two different crystals at 1.2 and 1.3 A resolution and refined to residuals of 0.169 and 0.176, respectively. Owing to a phase change, the c axis is double its room-t ...

    The structure of T(3)R(3) hexameric human insulin has been determined at 100 K from two different crystals at 1.2 and 1.3 A resolution and refined to residuals of 0.169 and 0.176, respectively. Owing to a phase change, the c axis is double its room-temperature value and the asymmetric unit contains two independent TR(f) insulin dimers. Compared with the orientation in the room-temperature structure, one dimer undergoes a rotation about the c axis of -5 degrees, while the second is rotated +4 degrees. A superposition of the backbone atoms of the two independent dimers shows that the C(alpha) atoms of five residues within the R(f)-state monomers are displaced by more than 1.0 A; smaller displacements are observed for the T-state monomers. Four zinc ions lie on the crystallographic threefold axis and each forms bonds to three symmetry-related HisB10 N(varepsilon2) atoms from the T- and R(f)-state trimers. While three of the zinc ions are tetrahedrally coordinated with a chloride ion completing the coordination sphere, mixed tetrahedral/octahedral coordination is observed for one of the T-state zinc ions. The three symmetry-related "phenolic binding sites" in one hexamer contain water molecules and a glycerol molecule, but the same sites in the second hexamer are occupied by a zinc ion coordinated to an alternate conformation of HisB10, a symmetry-related HisB5 and two chloride ions. Two additional and partially occupied zinc ion sites are observed at the interface between the two independent dimers. One zinc ion is coordinated by a T-state HisB5 of one dimer, an R-state HisB5 of the second dimer and two water molecules; the second zinc ion is coordinated by an alternate side-chain conformation of the T-state HisB5 and three water molecules. The carboxyl group of one GluB13 side chain, which exists in two discrete conformations, appears to be protonated, because short contacts exist to a second carboxyl group or to a carbonyl O atom.


    Related Citations: 
    • Structural stability in the 4-zinc human insulin hexamer
      Smith, G.D.,Swenson, D.C.,Dodson, E.J.,Dodson, G.G.,Reynolds, C.D.
      (1984) Proc.Natl.Acad.Sci.USA 81: 7093
    • X-ray Crystallographic Studies on Hexameric Insulins in the Presence of Helix-Stabilizing Agents, Thiocyanate, Methylparaben, and Phenol
      Whittingham, J.L.,Chaudhuri, S.,Dodson, E.J.,Moody, P.C.E.,Dodson, G.G.
      (1995) Biochemistry 34: 15553
    • Structure of 4-zinc insulin
      Bentley, G.,Dodson, E.,Dodson, G.G.,Hodgkin, D.,Mercola, D.
      (1976) Nature 261: 166
    • Crystallographic Evidence for Dual Coordination around Zinc in the T3R3 Human Insulin Hexamer
      Ciszak, E.,Smith, G.D.
      (1994) Biochemistry 33: 1512
    • The First Protein Crystal Structure Determined from High Resolution X-Ray Powder Diffraction Data: A Variant of T3R3 Human Insulin Zinc Complex Produced by Grinding
      Von Dreele, R.B.,Stephens, P.W.,Smith, G.D.,Blessing, R.H.
      (2000) Acta Crystallogr.,Sect.D 56: 1549


    Organizational Affiliation

    Hauptman-Woodward Medical Research Institute, 73 High Street, Buffalo, NY 14203, USA. smith@hwi.buffalo.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INSULIN A-CHAIN
A, C, E, G
21Homo sapiensGene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INSULIN B-CHAIN
B, D, F, H
30Homo sapiensGene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D, F, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACN
Query on ACN

Download SDF File 
Download CCD File 
F, G
ACETONE
C3 H6 O
CSCPPACGZOOCGX-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B, D, E, F, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
G
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.169 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 80.127α = 90.00
b = 80.127β = 90.00
c = 71.582γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model