8UHE

Structure of the far-red light-absorbing allophycocyanin core expressed during FaRLiP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the antenna complex expressed during far-red light photoacclimation in Synechococcus sp. PCC 7335.

Gisriel, C.J.Shen, G.Brudvig, G.W.Bryant, D.A.

(2023) J Biol Chem 300: 105590-105590

  • DOI: https://doi.org/10.1016/j.jbc.2023.105590
  • Primary Citation of Related Structures:  
    8UHE, 8UHI

  • PubMed Abstract: 

    Far-red light photoacclimation, or FaRLiP, is a facultative response exhibited by some cyanobacteria that allows them to absorb and utilize lower energy light (700-800 nm) than the wavelengths typically used for oxygenic photosynthesis (400-700 nm). During this process, three essential components of the photosynthetic apparatus are altered: photosystem I, photosystem II, and the phycobilisome. In all three cases, at least some of the chromophores found in these pigment-protein complexes are replaced by chromophores that have red-shifted absorbance relative to the analogous complexes produced in visible light. Recent structural and spectroscopic studies have elucidated important features of the two photosystems when altered to absorb and utilize far-red light, but much less is understood about the modified phycobiliproteins made during FaRLiP. We used single-particle, cryo-EM to determine the molecular structure of a phycobiliprotein core complex comprising allophycocyanin variants that absorb far-red light during FaRLiP in the marine cyanobacterium Synechococcus sp. PCC 7335. The structure reveals the arrangement of the numerous red-shifted allophycocyanin variants and the probable locations of the chromophores that serve as the terminal emitters in this complex. It also suggests how energy is transferred to the photosystem II complexes produced during FaRLiP. The structure additionally allows comparisons with other previously studied allophycocyanins to gain insights into how phycocyanobilin chromophores can be tuned to absorb far-red light. These studies provide new insights into how far-red light is harvested and utilized during FaRLiP, a widespread cyanobacterial photoacclimation mechanism.


  • Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, Connecticut, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ApcD5
A, E, G, M, O
A, E, G, M, O, Q
158Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WKI9 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Go to UniProtKB:  B4WKI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4WKI9
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ApcB2
B, D, F, H, L
B, D, F, H, L, N, P, R
161Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WKI8 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Go to UniProtKB:  B4WKI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4WKI8
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ApcD3181Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WKI4 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4WKI4
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ApcD2159Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WKI7 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4WKI7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ApcF169Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WIH2 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity Groups  
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UniProt GroupB4WIH2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ApcE2783Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WKI6 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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UniProt GroupB4WKI6
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ApcC67Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WI75 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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UniProt GroupB4WI75
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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 H]
BA [auth I]
CA [auth J]
FA [auth L]
GA [auth M]
AA [auth H],
BA [auth I],
CA [auth J],
FA [auth L],
GA [auth M],
HA [auth N],
IA [auth O],
JA [auth P],
KA [auth Q],
LA [auth R],
T [auth A],
U [auth B],
W [auth D],
X [auth E],
Y [auth F],
Z [auth G]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
M1V (Subject of Investigation/LOI)
Query on M1V

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DA [auth K],
V [auth C]
mesobiliverdin IX(alpha)
C33 H38 N4 O6
CXQHEXWJGZEPFP-BBROENKCSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth K]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B, D, F, H, L
B, D, F, H, L, N, P, R
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1613022
Department of Energy (DOE, United States)United StatesDE-FG02-05ER15646
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK99GM140174

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-03
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references