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- PDB-7s3d: Structure of photosystem I with bound ferredoxin from Synechococc... -

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Basic information

Entry
Database: PDB / ID: 7s3d
TitleStructure of photosystem I with bound ferredoxin from Synechococcus sp. PCC 7335 acclimated to far-red light
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 3
  • 2Fe-2S ferredoxin-type domain-containing protein
  • PSI subunit V
  • PSI-F
  • Photosystem I 16 kDa polypeptide
  • PsaC
  • PsaI2
  • PsaM
KeywordsPHOTOSYNTHESIS / Photosystem I / Far-red light photoacclimation / Chlorophyll f / Ferredoxin / PsaF / PsaJ
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Ferredoxin [2Fe-2S], plant / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Ferredoxin [2Fe-2S], plant / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / 2Fe-2S ferredoxin, iron-sulphur binding site / Electron transport accessory-like domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / Chlorophyll F / FE2/S2 (INORGANIC) CLUSTER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit II ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / Chlorophyll F / FE2/S2 (INORGANIC) CLUSTER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit II / 2Fe-2S ferredoxin-type domain-containing protein / Photosystem I reaction center subunit PsaK / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit IV
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7335 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsGisriel, C.J. / Flesher, D.A. / Shen, G. / Wang, J. / Ho, M. / Brudvig, G.W. / Bryant, D.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
National Science Foundation (NSF, United States)MCB-1613022 United States
CitationJournal: J Biol Chem / Year: 2022
Title: Structure of a photosystem I-ferredoxin complex from a marine cyanobacterium provides insights into far-red light photoacclimation.
Authors: Christopher J Gisriel / David A Flesher / Gaozhong Shen / Jimin Wang / Ming-Yang Ho / Gary W Brudvig / Donald A Bryant /
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 ...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.
History
DepositionSep 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 29, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: PsaC
D: Photosystem I 16 kDa polypeptide
E: Photosystem I reaction center subunit IV
F: PSI-F
I: PsaI2
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: PSI subunit V
M: PsaM
X: 2Fe-2S ferredoxin-type domain-containing protein
G: Photosystem I P700 chlorophyll a apoprotein A1
H: Photosystem I P700 chlorophyll a apoprotein A2
N: PsaC
O: Photosystem I 16 kDa polypeptide
P: Photosystem I reaction center subunit IV
Q: PSI-F
R: PsaI2
S: Photosystem I reaction center subunit IX
T: Photosystem I reaction center subunit PsaK
U: PSI subunit V
V: PsaM
W: 2Fe-2S ferredoxin-type domain-containing protein
a: Photosystem I P700 chlorophyll a apoprotein A1
b: Photosystem I P700 chlorophyll a apoprotein A2
c: PsaC
d: Photosystem I 16 kDa polypeptide
e: Photosystem I reaction center subunit IV
f: PSI-F
i: PsaI2
j: Photosystem I reaction center subunit IX
k: Photosystem I reaction center subunit PsaK
l: PSI subunit V
m: PsaM
x: 2Fe-2S ferredoxin-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,147,335453
Polymers827,61736
Non-polymers319,717417
Water5,999333
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 6 molecules AGaBHb

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PsaA / PsaA2


Mass: 86411.227 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WP20, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB / PsaB2


Mass: 83207.648 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WP21, photosystem I

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Protein , 6 types, 18 molecules CNcDOdFQfIRiLUlXWx

#3: Protein PsaC


Mass: 8809.169 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria)
#4: Protein Photosystem I 16 kDa polypeptide / Photosystem I reaction center subunit II / PsaD


Mass: 17051.336 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WFP8
#6: Protein PSI-F / Photosystem I reaction center subunit III / PsaF2


Mass: 18569.213 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WP24
#7: Protein PsaI2


Mass: 7668.838 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WP23
#10: Protein PSI subunit V / PSI-L / Photosystem I reaction center subunit XI / PsaL2


Mass: 18632.201 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WP22
#12: Protein 2Fe-2S ferredoxin-type domain-containing protein / PetJ


Mass: 10835.725 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WFX2

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Photosystem I reaction center subunit ... , 3 types, 9 molecules EPeJSjKTk

#5: Protein Photosystem I reaction center subunit IV / PsaE


Mass: 7955.112 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WSJ5
#8: Protein/peptide Photosystem I reaction center subunit IX / PsaJ2


Mass: 5170.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WP25
#9: Protein Photosystem I reaction center subunit PsaK / Photosystem I subunit X


Mass: 8195.834 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335 / References: UniProt: B4WL17

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Protein/peptide / Sugars , 2 types, 42 molecules MVm

#11: Protein/peptide PsaM


Mass: 3366.065 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria)
#21: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 12 types, 711 molecules

#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C55H72MgN4O5
#14: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: C55H72MgN4O5
#15: Chemical
ChemComp-F6C / Chlorophyll F / [methyl 9-ethenyl-14-ethyl-8-formyl-4,13,18-trimethyl-20-oxo-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,23,25-tetradehydro-24,26-dihydrophorbine-21-carboxylatato(2-)-kappa~4~N~23~,N~24~,N~25~,N~26~]magnesium


Mass: 905.457 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: C55H68MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C31H46O2
#17: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: Fe4S4
#18: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: C40H56
#19: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#20: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C45H86O10
#22: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#23: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#24: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Fe2S2
#25: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Far-red light-acclimated Photosystem I from Synechococcus sp. PCC 7335
Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 286672 / Symmetry type: POINT

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