7SA3

Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f.

Gisriel, C.J.Shen, G.Ho, M.Y.Kurashov, V.Flesher, D.A.Wang, J.Armstrong, W.H.Golbeck, J.H.Gunner, M.R.Vinyard, D.J.Debus, R.J.Brudvig, G.W.Bryant, D.A.

(2021) J Biol Chem 298: 101424-101424

  • DOI: https://doi.org/10.1016/j.jbc.2021.101424
  • Primary Citation of Related Structures:  
    7SA3

  • PubMed Abstract: 

    Far-red light (FRL) photoacclimation in cyanobacteria provides a selective growth advantage for some terrestrial cyanobacteria by expanding the range of photosynthetically active radiation to include far-red/near-infrared light (700-800 nm). During this photoacclimation process, photosystem II (PSII), the water:plastoquinone photooxidoreductase involved in oxygenic photosynthesis, is modified. The resulting FRL-PSII is comprised of FRL-specific core subunits and binds chlorophyll (Chl) d and Chl f molecules in place of several of the Chl a molecules found when cells are grown in visible light. These new Chls effectively lower the energy canonically thought to define the "red limit" for light required to drive photochemical catalysis of water oxidation. Changes to the architecture of FRL-PSII were previously unknown, and the positions of Chl d and Chl f molecules had only been proposed from indirect evidence. Here, we describe the 2.25 Å resolution cryo-EM structure of a monomeric FRL-PSII core complex from Synechococcus sp. PCC 7335 cells that were acclimated to FRL. We identify one Chl d molecule in the Chl D1 position of the electron transfer chain and four Chl f molecules in the core antenna. We also make observations that enhance our understanding of PSII biogenesis, especially on the acceptor side of the complex where a bicarbonate molecule is replaced by a glutamate side chain in the absence of the assembly factor Psb28. In conclusion, these results provide a structural basis for the lower energy limit required to drive water oxidation, which is the gateway for most solar energy utilization on earth.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem q(B) protein361Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WKH9 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Go to UniProtKB:  B4WKH9
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UniProt GroupB4WKH9
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center protein509Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WKI1 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Go to UniProtKB:  B4WKI1
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UniProt GroupB4WKI1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center protein482Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WKI2 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4WKI2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 protein352Synechococcus sp. PCC 7335Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for B4WKI3 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4WKI3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alpha80Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WII1 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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UniProt GroupB4WII1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit beta44Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WKJ2 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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UniProt GroupB4WKJ2
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IG [auth I]38Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WM03 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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UniProt GroupB4WM03
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KH [auth K]45Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WR12 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
UnknownI [auth N]23Synechococcus sp. PCC 7335Mutation(s): 0 
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AB [auth C],
IA [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
F6C (Subject of Investigation/LOI)
Query on F6C

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EA [auth B],
SA [auth C],
V [auth B],
Y [auth B]
Chlorophyll F
C55 H68 Mg N4 O6
YUTLCKLMRUVWDE-FOFJUSMOSA-M
CL7 (Subject of Investigation/LOI)
Query on CL7

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M [auth A]CHLOROPHYLL D
C54 H70 Mg N4 O6
FBCRYORFRGRJBC-ACDPFEIMSA-L
CLA
Query on CLA

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AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
FA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
FA [auth B],
FB [auth D],
GA [auth B],
GB [auth D],
L [auth A],
MA [auth C],
N [auth A],
NA [auth C],
OA [auth C],
P [auth A],
PA [auth C],
QA [auth C],
RA [auth C],
T [auth B],
TA [auth C],
U [auth B],
UA [auth C],
VA [auth C],
W [auth B],
WA [auth C],
X [auth B],
XA [auth C],
YA [auth C],
Z [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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EB [auth D],
O [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
LMG
Query on LMG

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JA [auth B],
KB [auth D]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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IB [auth D]2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
Query on LHG

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JB [auth D]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM

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MB [auth F]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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CB [auth C],
HA [auth B],
HB [auth D],
Q [auth A],
ZA [auth C]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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BB [auth C]
KA [auth B]
LA [auth B]
LB [auth D]
R [auth A]
BB [auth C],
KA [auth B],
LA [auth B],
LB [auth D],
R [auth A],
S [auth A]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE2
Query on FE2

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DB [auth D]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

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J [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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K [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Database references