7S3D

Structure of photosystem I with bound ferredoxin from Synechococcus sp. PCC 7335 acclimated to far-red light


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a photosystem I-ferredoxin complex from a marine cyanobacterium provides insights into far-red light photoacclimation.

Gisriel, C.J.Flesher, D.A.Shen, G.Wang, J.Ho, M.Y.Brudvig, G.W.Bryant, D.A.

(2021) J Biol Chem 298: 101408-101408

  • DOI: https://doi.org/10.1016/j.jbc.2021.101408
  • Primary Citation of Related Structures:  
    7S3D

  • PubMed Abstract: 

    Far-red light photoacclimation exhibited by some cyanobacteria allows these organisms to use the far-red region of the solar spectrum (700-800 nm) for photosynthesis. Part of this process includes the replacement of six photosystem I (PSI) subunits with isoforms that confer the binding of chlorophyll (Chl) f molecules that absorb far-red light (FRL). However, the exact sites at which Chl f molecules are bound are still challenging to determine. To aid in the identification of Chl f-binding sites, we solved the cryo-EM structure of PSI from far-red light-acclimated cells of the cyanobacterium Synechococcus sp. PCC 7335. We identified six sites that bind Chl f with high specificity and three additional sites that are likely to bind Chl f at lower specificity. All of these binding sites are in the core-antenna regions of PSI, and Chl f was not observed among the electron transfer cofactors. This structural analysis also reveals both conserved and nonconserved Chl f-binding sites, the latter of which exemplify the diversity in FRL-PSI among species. We found that the FRL-PSI structure also contains a bound soluble ferredoxin, PetF1, at low occupancy, which suggests that ferredoxin binds less transiently than expected according to the canonical view of ferredoxin-binding to facilitate electron transfer. We suggest that this may result from structural changes in FRL-PSI that occur specifically during FRL photoacclimation.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
M [auth G],
Y [auth a]
782Synechococcus sp. PCC 7335Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for B4WP20 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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UniProt GroupB4WP20
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
N [auth H],
Z [auth b]
743Synechococcus sp. PCC 7335Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PsaCAA [auth c],
C,
O [auth N]
81Synechococcus sp. PCC 7335Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I 16 kDa polypeptideBA [auth d],
D,
P [auth O]
155Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WFP8 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVCA [auth e],
E,
Q [auth P]
71Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WSJ5 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-FDA [auth f],
F,
R [auth Q]
168Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WP24 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PsaI2EA [auth i],
G [auth I],
S [auth R]
70Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXFA [auth j],
H [auth J],
T [auth S]
46Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WP25 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKGA [auth k],
I [auth K],
U [auth T]
84Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WL17 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PSI subunit VHA [auth l],
J [auth L],
V [auth U]
174Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B4WP22 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PsaMIA [auth m],
K [auth M],
W [auth V]
31Synechococcus sp. PCC 7335Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
2Fe-2S ferredoxin-type domain-containing proteinJA [auth x],
L [auth X],
X [auth W]
99Synechococcus sp. PCC 7335Mutation(s): 0 
UniProt
Find proteins for B4WFX2 (Synechococcus sp. (strain ATCC 29403 / PCC 7335))
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F6C (Subject of Investigation/LOI)
Query on F6C

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BD [auth B]
FE [auth B]
FO [auth b]
GE [auth B]
HB [auth A]
Chlorophyll F
C55 H68 Mg N4 O6
YUTLCKLMRUVWDE-FOFJUSMOSA-M
CLA
Query on CLA

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AB [auth A]
AC [auth A]
AD [auth B]
AE [auth B]
AG [auth G]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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CL [auth a],
KA [auth A],
TF [auth G]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG

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AF [auth I]
AK [auth H]
EN [auth a]
JK [auth R]
JP [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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CN [auth a]
CQ [auth l]
DN [auth a]
DQ [auth l]
KC [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR

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AN [auth a]
AQ [auth l]
BN [auth a]
BQ [auth l]
CP [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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AL [auth V]
BF [auth I]
BK [auth H]
CK [auth H]
DK [auth H]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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BP [auth b]
CC [auth A]
JE [auth B]
LH [auth G]
SJ [auth H]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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DC [auth A]
FK [auth N]
GK [auth N]
MH [auth G]
OP [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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BL [auth W],
KQ [auth x],
SF [auth X]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CA
Query on CA

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EF [auth L],
NK [auth U],
WP [auth l]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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AI [auth G],
JN [auth a],
RC [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-FG02-05ER15646
National Science Foundation (NSF, United States)United StatesMCB-1613022

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 1.2: 2021-12-29
    Changes: Database references
  • Version 1.3: 2024-06-05
    Changes: Data collection