1B33

STRUCTURE OF LIGHT HARVESTING COMPLEX OF ALLOPHYCOCYANIN ALPHA AND BETA CHAINS/CORE-LINKER COMPLEX AP*LC7.8

• PDB DOI:  https://doi.org/10.2210/pdb1B33/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Mastigocladus laminosus
• Mutation(s): Yes 


• Deposited: 1998-12-15 Released: 1999-02-23 
• Deposition Author(s): Reuter, W., Wiegand, G., Huber, R., Than, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.256 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 

Literature

Structural analysis at 2.2 A of orthorhombic crystals presents the asymmetry of the allophycocyanin-linker complex, AP.LC7.8, from phycobilisomes of Mastigocladus laminosus.

Reuter, W., Wiegand, G., Huber, R., Than, M.E.

(1999) Proc Natl Acad Sci U S A 96: 1363-1368

• PubMed: 9990029 
• DOI: https://doi.org/10.1073/pnas.96.4.1363
• Primary Citation of Related Structures:  
  1B33


• PubMed Abstract: 
  

An electrophoretically purified allophycocyanin-linker complex, AP. LC7.8, from phycobilisomes of Mastigocladus laminosus has been crystallized in the orthorhombic space group P212121. Cryocrystallographic x-ray measurements enabled the structural analysis of the complex at a resolution of 2.2 A. The asymmetric unit contains two side-to-side associated "trimeric" (alphabeta)3 allophycocyanin complexes comprising the linker polypeptide in a defined orientation inside the trimer. The linker representing a protein fold related to the prosegment of procarboxypeptidase A is in contact with only two of the three beta-subunits and directly interacts with the corresponding chromophores of these proteins. In addition to a modulation of the chromophores' spectral properties, the linker polypeptide attracts the alphabeta-subcomplexes, thereby bringing the beta-chromophores closer together. These results will enable interpretations of energy-transfer mechanisms within phycobiliproteins.

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Related Citations: 

• Isolation, Crystallization, Crystal Structure Analysis and Refinement of Allophycocyanin from the Cyanobacterium Spirulina Platensis at 2.3 A Resolution
  Brejc, K., Ficner, R., Huber, R., Steinbacher, S.
  (1995) J Mol Biol 249: 424

• Minor Polypeptides from the Cyanobacterium Mastigocladus Laminosus
  Fueglistaller, P., Ruembli, R., Suter, F., Zuber, H.
  (1984) Hoppe Seylers Z Physiol Chem 365: 1085

• The Complete Amino Acid Sequence of Both Subunits of Allophycocyanin, a Light Harvesting Protein-Pigment Complex from the Cyanobacterium Mastigocladus Laminosus
  Sidler, W., Gysi, J., Isker, E., Zuber, H.
  (1981) Hoppe Seylers Z Physiol Chem 362: 611

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82158 Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A3B3C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A6B1 Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Hetero 6-mer - A3B3 

Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Hetero 6-mer - A3B3 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A3B3C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A6B1 Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Hetero 6-mer - A3B3 

Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 230.13 kDa 
• Atom Count: 17,502 
• Modelled Residue Count: 2,060 
• Deposited Residue Count: 2,060 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALLOPHYCOCYANIN, ALPHA CHAIN	A, C, E, H, J, L	160	Mastigocladus laminosus	Mutation(s): 0  Gene Names: apcA
UniProt
Find proteins for P00315 (Mastigocladus laminosus) Explore P00315  Go to UniProtKB:  P00315

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALLOPHYCOCYANIN, BETA CHAIN	B, D, F, I, K, M	161	Mastigocladus laminosus	Mutation(s): 1  Gene Names: apcB
UniProt
Find proteins for P00318 (Mastigocladus laminosus) Explore P00318  Go to UniProtKB:  P00318

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE	G [auth N], N [auth O]	67	Mastigocladus laminosus	Mutation(s): 0  Gene Names: apcC
UniProt
Find proteins for P20116 (Mastigocladus laminosus) Explore P20116  Go to UniProtKB:  P20116

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC	AA [auth K], BA [auth L], DA [auth M], Q [auth C], S [auth D], T [auth E], V [auth F], W [auth H], X [auth I], Y [auth J]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N
BLA	O [auth A], P [auth B]	BILIVERDINE IX ALPHA C33 H34 N4 O6 GWZYPXHJIZCRAJ-SRVCBVSDSA-N
BO4	CA [auth L], R [auth C], U [auth E], Z [auth J]	BORATE ION B H4 O4 KCFLOKKYWBPKFN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.256 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.12	α = 90
b = 151.9	β = 90
c = 137.85	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-23 
Deposition Author(s): Reuter, W., Wiegand, G., Huber, R., Than, M.E.

Revision History  

• Version 1.0: 1999-02-23
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-20
  Changes: Data collection, Refinement description