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- PDB-9e0j: Structure and evolution of Photosystem I in the early-branching c... -

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Basic information

Entry
Database: PDB / ID: 9e0j
TitleStructure and evolution of Photosystem I in the early-branching cyanobacterium Anthocerotibacter panamensis
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 7
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem I / evolution / thylakoid-free / chlorophyll / cyanobacteria
Function / homologyMenaquinone-4 / beta,beta-carotene-4,4'-dione / BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesAnthocerotibacter panamensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsGisriel, C.J. / Ho, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM140174 United States
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structure and evolution of photosystem I in the early-branching cyanobacterium .
Authors: Han-Wei Jiang / Christopher J Gisriel / Tanai Cardona / David A Flesher / Gary W Brudvig / Ming-Yang Ho /
Abstract: Thylakoid-free cyanobacteria are thought to preserve ancestral traits of early-evolving organisms capable of oxygenic photosynthesis. However, and until recently, photosynthesis studies in thylakoid- ...Thylakoid-free cyanobacteria are thought to preserve ancestral traits of early-evolving organisms capable of oxygenic photosynthesis. However, and until recently, photosynthesis studies in thylakoid-free cyanobacteria were only possible in the model strain , limiting our understanding of photosynthesis evolution. Here, we report the isolation, biochemical characterization, cryo-EM structure, and phylogenetic analysis of photosystem I (PSI) from a recently discovered thylakoid-free cyanobacterium, , a distant relative of the genus . We find that PSI exhibits a distinct carotenoid composition and has one conserved low-energy chlorophyll site, which was lost in . Furthermore, PSI in thylakoid-free cyanobacteria has changed at the sequence level to a degree comparable to that of other strains, yet its subunit composition and oligomeric form might be identical to that of the most recent common ancestor of cyanobacteria. This study therefore provides a glimpse into the ancient evolution of photosynthesis.
History
DepositionOct 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Photosystem I P700 chlorophyll a apoprotein A1
T: Photosystem I reaction center subunit XII
H: Photosystem I P700 chlorophyll a apoprotein A2
K: Photosystem I iron-sulfur center
N: Photosystem I reaction center subunit II
O: Photosystem I reaction center subunit IV
P: Photosystem I reaction center subunit III
Q: Photosystem I reaction center subunit VIII
R: Photosystem I reaction center subunit IX
S: Photosystem I reaction center subunit XI
a: Photosystem I P700 chlorophyll a apoprotein A1
m: Photosystem I reaction center subunit XII
b: Photosystem I P700 chlorophyll a apoprotein A2
c: Photosystem I iron-sulfur center
d: Photosystem I reaction center subunit II
e: Photosystem I reaction center subunit IV
f: Photosystem I reaction center subunit III
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
l: Photosystem I reaction center subunit XI
A: Photosystem I P700 chlorophyll a apoprotein A1
M: Photosystem I reaction center subunit XII
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: Photosystem I reaction center subunit XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,039,560396
Polymers747,63830
Non-polymers291,922366
Water9,998555
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1


Mass: 86732.508 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#3: Protein Photosystem I P700 chlorophyll a apoprotein A2


Mass: 82935.758 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)

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Photosystem I reaction center subunit ... , 7 types, 21 molecules TmMNdDOeEPfFQiIRjJSlL

#2: Protein/peptide Photosystem I reaction center subunit XII


Mass: 3319.953 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#5: Protein Photosystem I reaction center subunit II


Mass: 15481.709 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#6: Protein Photosystem I reaction center subunit IV


Mass: 7236.996 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#7: Protein Photosystem I reaction center subunit III


Mass: 19575.764 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#8: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3712.463 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#9: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4364.390 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#10: Protein Photosystem I reaction center subunit XI


Mass: 17047.908 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)

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Protein / Sugars , 2 types, 6 molecules KcC

#19: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Protein Photosystem I iron-sulfur center


Mass: 8805.158 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)

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Non-polymers , 9 types, 918 molecules

#11: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#12: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 264 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#13: Chemical
ChemComp-1L3 / Menaquinone-4 / vitamin K2


Mass: 444.648 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H40O2
#14: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#15: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 66 / Source method: obtained synthetically / Formula: C40H56
#16: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#17: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H52O2 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10
#20: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: Photosystem I from Anthocerotibacter panamensis / Type: COMPLEX / Entity ID: #1, #3-#10, #2 / Source: NATURAL
Source (natural)Organism: Anthocerotibacter panamensis (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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 403080 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01573191
ELECTRON MICROSCOPYf_angle_d2.523103734
ELECTRON MICROSCOPYf_dihedral_angle_d31.07417712
ELECTRON MICROSCOPYf_chiral_restr0.1059231
ELECTRON MICROSCOPYf_plane_restr0.01812459

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