1V2B

Crystal Structure of PsbP Protein in the Oxygen-Evolving Complex of Photosystem II from Higher Plants

• PDB DOI: https://doi.org/10.2210/pdb1V2B/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Nicotiana tabacum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-10-14 Released: 2004-05-18 
• Deposition Author(s): Ifuku, K., Nakatsu, T., Kato, H., Sato, F., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.207 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 

Literature

Crystal structure of the PsbP protein of photosystem II from Nicotiana tabacum

Ifuku, K., Nakatsu, T., Kato, H., Sato, F.

(2004) EMBO Rep 5: 362-367

• PubMed: 15031714 
• DOI: https://doi.org/10.1038/sj.embor.7400113
• Primary Citation of Related Structures:  
  1V2B


• PubMed Abstract: 
  

  PsbP is a membrane-extrinsic subunit of the water-oxidizing complex photosystem II (PS II). The evolutionary origin of PsbP has long been a mystery because it specifically exists in higher plants and green algae but not in cyanobacteria. We report here the crystal structure of PsbP from Nicotiana tabacum at a resolution of 1.6 A. Its structure is mainly composed of beta-sheet, and is not similar to any structures in cyanobacterial PS II. However, the electrostatic surface potential of PsbP is similar to that of cyanobacterial PsbV (cyt c(550)), which has a function similar to PsbP. A structural homology search with the DALI algorithm indicated that the folding of PsbP is very similar to that of Mog1p, a regulatory protein for the nuclear transport of Ran GTPase. The structure of PsbP provides insight into its novel function in GTP-regulated metabolism in PS II.

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Organizational Affiliation: 

Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.37 kDa 
• Atom Count: 2,795 
• Modelled Residue Count: 299 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
23-kDa polypeptide of photosystem II oxygen-evolving complex	A, B	177	Nicotiana tabacum	Mutation(s): 0  Gene Names: psbp
UniProt
Find proteins for P18212 (Nicotiana tabacum) Explore P18212  Go to UniProtKB:  P18212

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	C [auth A], E [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.207 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.52	α = 90
b = 90.442	β = 90
c = 52.635	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-18 
Deposition Author(s): Ifuku, K., Nakatsu, T., Kato, H., Sato, F., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2004-05-18
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Structure summary