Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.53 kDa 
• Atom Count: 2451 
• Modelled Residue Count: 293 
• Deposited Residue Count: 314 
• Unique protein chains: 1

4XXI

Crystal structure of the Bilin-binding domain of phycobilisome core-membrane linker ApcE

• PDB DOI: 10.2210/pdb4XXI/pdb

• Classification: TRANSFERASE
• Organism(s): Nostoc sp. PCC 7120 = FACHB-418
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-30 Released: 2015-12-16 
• Deposition Author(s): Tang, K., Ding, W.-L., Hoppner, A., Gartner, W., Zhao, K.-H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 

Literature

The terminal phycobilisome emitter, LCM: A light-harvesting pigment with a phytochrome chromophore

Tang, K., Ding, W.-L., Hoppner, A., Zhao, C., Zhang, L., Hontani, Y., Kennis, J.T.M., Gartner, W., Scheer, H., Zhou, M., Zhao, K.-H.

(2015) Proc Natl Acad Sci U S A 112: 15880-15885

• PubMed: 26669441 
• DOI: 10.1073/pnas.1519177113
• Primary Citation of Related Structures:  
  4XXI, 4XXK


• PubMed Abstract: 
  

Photosynthesis relies on energy transfer from light-harvesting complexes to reaction centers. Phycobilisomes, the light-harvesting antennas in cyanobacteria and red algae, attach to the membrane via the multidomain core-membrane linker, L(CM). The chromophore domain of L(CM) forms a bottleneck for funneling the harvested energy either productively to reaction centers or, in case of light overload, to quenchers like orange carotenoid protein (OCP) that prevent photodamage. The crystal structure of the solubly modified chromophore domain from Nostoc sp. PCC7120 was resolved at 2.2 Å. Although its protein fold is similar to the protein folds of phycobiliproteins, the phycocyanobilin (PCB) chromophore adopts ZZZssa geometry, which is unknown among phycobiliproteins but characteristic for sensory photoreceptors (phytochromes and cyanobacteriochromes). However, chromophore photoisomerization is inhibited in L(CM) by tight packing. The ZZZssa geometry of the chromophore and π-π stacking with a neighboring Trp account for the functionally relevant extreme spectral red shift of L(CM). Exciton coupling is excluded by the large distance between two PCBs in a homodimer and by preservation of the spectral features in monomers. The structure also indicates a distinct flexibility that could be involved in quenching. The conclusions from the crystal structure are supported by femtosecond transient absorption spectra in solution.

---

Organizational Affiliation: 

State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycobiliprotein ApcE	A, B	157	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0  Gene Names: apcE, alr0020 EC: 4
UniProt
Find proteins for P80559 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore P80559  Go to UniProtKB:  P80559

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC	C [auth A], D [auth B]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.251 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.356	α = 90
b = 80.552	β = 90
c = 115.449	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data processing
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-30 
• Released Date: 2015-12-16 
Deposition Author(s): Tang, K., Ding, W.-L., Hoppner, A., Gartner, W., Zhao, K.-H.

Revision History  

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2016-01-13
  Changes: Database references, Structure summary
• Version 1.2: 2018-05-16
  Changes: Data collection, Derived calculations