4RI3

Crystal structure of DCCD-modified PsbS from spinach


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of the PsbS protein essential for photoprotection in plants.

Fan, M.Li, M.Liu, Z.Cao, P.Pan, X.Zhang, H.Zhao, X.Zhang, J.Chang, W.

(2015) Nat Struct Mol Biol 22: 729-735

  • DOI: 10.1038/nsmb.3068
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The photosystem II protein PsbS has an essential role in qE-type nonphotochemical quenching, which protects plants from photodamage under excess light conditions. qE is initiated by activation of PsbS by low pH, but the mechanism of PsbS action remai ...

    The photosystem II protein PsbS has an essential role in qE-type nonphotochemical quenching, which protects plants from photodamage under excess light conditions. qE is initiated by activation of PsbS by low pH, but the mechanism of PsbS action remains elusive. Here we report the low-pH crystal structures of PsbS from spinach in its free form and in complex with the qE inhibitor N,N'-dicyclohexylcarbodiimide (DCCD), revealing that PsbS adopts a unique folding pattern, and, unlike other members of the light-harvesting-complex superfamily, it is a noncanonical pigment-binding protein. Structural and biochemical evidence shows that both active and inactive PsbS form homodimers in the thylakoid membranes, and DCCD binding disrupts the lumenal intermolecular hydrogen bonds of the active PsbS dimer. Activation of PsbS by low pH during qE may involve a conformational change associated with altered lumenal intermolecular interactions of the PsbS dimer.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 22 kDa protein, chloroplastic
A, B
212Spinacia oleraceaMutation(s): 0 
Gene Names: PSBS
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photoprotection Proteins
Protein: 
PsbS photoprotection protein
Find proteins for Q02060 (Spinacia oleracea)
Go to UniProtKB:  Q02060
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BNG
Query on BNG

Download CCD File 
A, B
B-NONYLGLUCOSIDE
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
DCW
Query on DCW

Download CCD File 
A, B
DICYCLOHEXYLUREA
C13 H24 N2 O
ADFXKUOMJKEIND-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG

Download CCD File 
A, B
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.704α = 90
b = 77.697β = 90
c = 93.159γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-08-26
    Changes: Database references
  • Version 1.2: 2015-09-16
    Changes: Database references