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PDBsum entry 1g7b

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protein ligands metals Protein-protein interface(s) links
Hormone/growth factor PDB id
1g7b
Jmol
Contents
Protein chains
21 a.a.
30 a.a. *
29 a.a. *
28 a.a. *
Ligands
GOL
ACN
Metals
_CL ×7
_ZN ×7
Waters ×241
* Residue conservation analysis
PDB id:
1g7b
Name: Hormone/growth factor
Title: 1.3 a structure of t3r3 human insulin at 100 k
Structure: Insulin a-chain. Chain: a, c, e, g. Fragment: a-chain. Engineered: yes. Insulin b-chain. Chain: b, d, f, h. Fragment: b-chain. Engineered: yes
Source: Synthetic: yes. Other_details: this sequence occurs naturally in homo sapie (human). (Human)
Biol. unit: Dodecamer (from PDB file)
Resolution:
1.30Å     R-factor:   0.176     R-free:   0.204
Authors: G.D.Smith,W.A.Pangborn,R.H.Blessing
Key ref:
G.D.Smith et al. (2001). Phase changes in T(3)R(3)(f) human insulin: temperature or pressure induced? Acta Crystallogr D Biol Crystallogr, 57, 1091-1100. PubMed id: 11468392 DOI: 10.1107/S0907444901007685
Date:
09-Nov-00     Release date:   03-Aug-01    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P01308  (INS_HUMAN) -  Insulin
Seq:
Struc:
110 a.a.
21 a.a.
Protein chains
Pfam   ArchSchema ?
P01308  (INS_HUMAN) -  Insulin
Seq:
Struc:
110 a.a.
30 a.a.
Protein chain
Pfam   ArchSchema ?
P01308  (INS_HUMAN) -  Insulin
Seq:
Struc:
110 a.a.
29 a.a.
Protein chain
Pfam   ArchSchema ?
P01308  (INS_HUMAN) -  Insulin
Seq:
Struc:
110 a.a.
28 a.a.
Key:    PfamA domain  Secondary structure

 

 
DOI no: 10.1107/S0907444901007685 Acta Crystallogr D Biol Crystallogr 57:1091-1100 (2001)
PubMed id: 11468392  
 
 
Phase changes in T(3)R(3)(f) human insulin: temperature or pressure induced?
G.D.Smith, W.A.Pangborn, R.H.Blessing.
 
  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-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.
 
  Selected figure(s)  
 
Figure 6.
Figure 6 SETOR drawing (Evans, 1993[Evans, S. V. (1993). J. Mol. Graph. 6, 244-245.]) of the interface between the two independent dimers, illustrating the coordination to the two zinc ions. A chains are colored red, B chains green, water molecules dark blue, zinc ions magenta, histidine side chains cyan and disulfide bridges yellow.
Figure 7.
Figure 7 Interactions between the GluB13 side chains in (a) 1trz; (b) hexamer 1 of the present study and (c) hexamer 2 of the present study. In (c), the side chains of SerB9.3 are colored cyan; the black dashed lines illustrate the 2.54 contact between GluB13.4 O 1 and GluB13.3 O 2 and the 2.73 contact between the carbonyl O of SerB9.3 and O 2 of the second alternate orientation of GluB13.4.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 1091-1100) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20823552 F.Pavelcík, and J.Václavík (2010).
Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments.
  Acta Crystallogr D Biol Crystallogr, 66, 1012-1023.  
19462064 M.T.Weller, P.F.Henry, V.P.Ting, and C.C.Wilson (2009).
Crystallography of hydrogen-containing compounds: realizing the potential of neutron powder diffraction.
  Chem Commun (Camb), (), 2973-2989.  
19527679 S.Xia, and J.D.Robertus (2009).
Effect of divalent ions on the minimal relaxase domain of MobA.
  Arch Biochem Biophys, 488, 42-47.  
18156682 I.Margiolaki, and J.P.Wright (2008).
Powder crystallography on macromolecules.
  Acta Crystallogr A, 64, 169-180.  
18156673 W.I.David, and K.Shankland (2008).
Structure determination from powder diffraction data.
  Acta Crystallogr A, 64, 52-64.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.