Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

Global Symmetry: Octahedral - O  (3D View)
Global Stoichiometry: Hetero 48-mer - A24B24 Pseudo Symmetry: Octahedral - O  (3D View)
Pseudo Stoichiometry: Homo 48-mer - A48 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 113.59 kDa 
• Atom Count: 9,246 
• Modelled Residue Count: 969 
• Deposited Residue Count: 984 
• Unique protein chains: 2

 4PO5

Crystal structure of allophycocyanin B from Synechocystis PCC 6803

• PDB DOI:  https://doi.org/10.2210/pdb4PO5/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Mutation(s): No 


• Deposited: 2014-02-24 Released: 2014-10-29 
• Deposition Author(s): Pang, P.P., Dong, L.L., Sun, Y.F., Zeng, X.L., Ding, W.L., Scheer, H., Yang, X., Zhao, K.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.194 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Literature

The structure of allophycocyanin B from Synechocystis PCC 6803 reveals the structural basis for the extreme redshift of the terminal emitter in phycobilisomes.

Peng, P.P., Dong, L.L., Sun, Y.F., Zeng, X.L., Ding, W.L., Scheer, H., Yang, X., Zhao, K.H.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2558-2569

• PubMed: 25286841 
• DOI: https://doi.org/10.1107/S1399004714015776
• Primary Citation of Related Structures:  
  4PO5


• PubMed Abstract: 
  

Allophycocyanin B (AP-B) is one of the two terminal emitters in phycobilisomes, the unique light-harvesting complexes of cyanobacteria and red algae. Its low excitation-energy level and the correspondingly redshifted absorption and fluorescence emission play an important role in funnelling excitation energy from the hundreds of chromophores of the extramembraneous phycobilisome to the reaction centres within the photosynthetic membrane. In the absence of crystal structures of these low-abundance terminal emitters, the molecular basis for the extreme redshift and directional energy transfer is largely unknown. Here, the crystal structure of trimeric AP-B [(ApcD/ApcB)3] from Synechocystis sp. PCC 6803 at 1.75 Å resolution is reported. In the crystal lattice, eight trimers of AP-B form a porous, spherical, 48-subunit assembly of 193 Å in diameter with an internal cavity of 1.1 × 10(6) Å(3). While the overall structure of trimeric AP-B is similar to those reported for many other phycobiliprotein trimers, the chromophore pocket of the α-subunit, ApcD, has more bulky residues that tightly pack the phycocyanobilin (PCB). Ring D of the chromophores is further stabilized by close interactions with ApcB from the adjacent monomer. The combined contributions from both subunits render the conjugated rings B, C and D of the PCB in ApcD almost perfectly coplanar. Together with mutagenesis data, it is proposed that the enhanced planarity effectively extends the conjugation system of PCB and leads to the redshifted absorption (λmax = 669 nm) and fluorescence emission (679 nm) of the ApcD chromophore in AP-B, thereby enabling highly efficient energy transfer from the phycobilisome core to the reaction centres.

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Organizational Affiliation: 

State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophycocyanin subunit alpha-B	A, C, E	167	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: apcD, sll0928
UniProt
Find proteins for P72870 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P72870  Go to UniProtKB:  P72870

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophycocyanin beta chain	B, D, F	161	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: apcB, slr1986
UniProt
Find proteins for Q01952 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore Q01952  Go to UniProtKB:  Q01952

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC	BA [auth F], G [auth A], J [auth B], P [auth C], S [auth D], Y [auth E]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N
SO4	AA [auth E], CA [auth F], DA [auth F], EA [auth F], FA [auth F], GA [auth F], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], T [auth D], U [auth D], V [auth D], W [auth D], X [auth D], Z [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN	B, D, F	L-PEPTIDE LINKING	C5 H10 N2 O3		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.194 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.293	α = 90
b = 184.293	β = 90
c = 260.954	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Pang, P.P., Dong, L.L., Sun, Y.F., Zeng, X.L., Ding, W.L., Scheer, H., Yang, X., Zhao, K.H.

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release