1B33

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


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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALLOPHYCOCYANIN, ALPHA CHAIN
A, C, E, H, J
A, C, E, H, J, L
160Mastigocladus laminosusMutation(s): 0 
UniProt
Find proteins for P00315 (Mastigocladus laminosus)
Explore P00315 
Go to UniProtKB:  P00315
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00315
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALLOPHYCOCYANIN, BETA CHAIN
B, D, F, I, K
B, D, F, I, K, M
161Mastigocladus laminosusMutation(s): 1 
UniProt
Find proteins for P00318 (Mastigocladus laminosus)
Explore P00318 
Go to UniProtKB:  P00318
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00318
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDEG [auth N],
N [auth O]
67Mastigocladus laminosusMutation(s): 0 
UniProt
Find proteins for P20116 (Mastigocladus laminosus)
Explore P20116 
Go to UniProtKB:  P20116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20116
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC
Query on CYC

Download Ideal Coordinates CCD File 
AA [auth K]
BA [auth L]
DA [auth M]
Q [auth C]
S [auth D]
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
Query on BLA

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O [auth A],
P [auth B]
BILIVERDINE IX ALPHA
C33 H34 N4 O6
GWZYPXHJIZCRAJ-SRVCBVSDSA-N
BO4
Query on BO4

Download Ideal Coordinates CCD File 
CA [auth L],
R [auth C],
U [auth E],
Z [auth J]
BORATE ION
B H4 O4
KCFLOKKYWBPKFN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B, D, F, I, K
B, D, F, I, K, M
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
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 = 176.12α = 90
b = 151.9β = 90
c = 137.85γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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