1TKW

The transient complex of poplar plastocyanin with turnip cytochrome f determined with paramagnetic NMR


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 104 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The transient complex of poplar plastocyanin with cytochrome f: effects of ionic strength and pH

Lange, C.Cornvik, T.Diaz-Moreno, I.Ubbink, M.

(2005) Biochim.Biophys.Acta 1707: 179-188

  • DOI: 10.1016/j.bbabio.2004.12.002

  • PubMed Abstract: 
  • The orientation of poplar plastocyanin in the complex with turnip cytochrome f has been determined by rigid-body calculations using restraints from paramagnetic NMR measurements. The results show that poplar plastocyanin interacts with cytochrome f w ...

    The orientation of poplar plastocyanin in the complex with turnip cytochrome f has been determined by rigid-body calculations using restraints from paramagnetic NMR measurements. The results show that poplar plastocyanin interacts with cytochrome f with the hydrophobic patch of plastocyanin close to the heme region on cytochrome f and via electrostatic interactions between the charged patches on both proteins. Plastocyanin is tilted relative to the orientation reported for spinach plastocyanin, resulting in a longer distance between iron and copper (13.9 A). With increasing ionic strength, from 0.01 to 0.11 M, all observed chemical-shift changes decrease uniformly, supporting the idea that electrostatic forces contribute to complex formation. There is no indication for a rearrangement of the transient complex in this ionic strength range, contrary to what had been proposed earlier on the basis of kinetic data. By decreasing the pH from pH 7.7 to pH 5.5, the complex is destabilized. This may be attributed to the protonation of the conserved acidic patches or the copper ligand His87 in poplar plastocyanin, which are shown to have similar pK(a) values. The results are interpreted in a two-step model for complex formation.


    Organizational Affiliation

    Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plastocyanin A
A
99Populus nigraMutation(s): 0 
Gene Names: PETE
Find proteins for P00299 (Populus nigra)
Go to UniProtKB:  P00299
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome f
B
252Brassica rapa subsp. rapaMutation(s): 0 
Gene Names: petA
Find proteins for P36438 (Brassica rapa subsp. rapa)
Go to UniProtKB:  P36438
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 104 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 
  • Olderado: 1TKW Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-24
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance