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Entry
Database: EMDB / ID: EMD-47359
TitleStructure and evolution of Photosystem I in the early-branching cyanobacterium Anthocerotibacter panamensis
Map datasharpened and masked main map
Sample
  • Complex: Photosystem I from Anthocerotibacter panamensis
    • Protein or peptide: x 10 types
  • Ligand: x 10 types
KeywordsPhotosystem I / evolution / thylakoid-free / chlorophyll / cyanobacteria / PHOTOSYNTHESIS
Biological speciesAnthocerotibacter panamensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsGisriel CJ / Ho M
Funding support United States, 2 items
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, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47359.png

Downloads & links

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Map

FileDownload / File: emd_47359.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened and masked main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00112
Minimum - Maximum-0.03864714 - 0.065710194
Average (Standard dev.)0.00011172579 (±0.0022438788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened unmasked

Fileemd_47359_additional_1.map
Annotationunsharpened unmasked
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half 2

Fileemd_47359_half_map_1.map
AnnotationHalf 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 1

Fileemd_47359_half_map_2.map
AnnotationHalf 1
Projections & Slices
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Slices (1/2)
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Sample components

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Entire : Photosystem I from Anthocerotibacter panamensis

EntireName: Photosystem I from Anthocerotibacter panamensis
Components
  • Complex: Photosystem I from Anthocerotibacter panamensis
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit II
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: CHLOROPHYLL A
  • Ligand: Menaquinone-4
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: beta,beta-carotene-4,4'-dione
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: water

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Supramolecule #1: Photosystem I from Anthocerotibacter panamensis

SupramoleculeName: Photosystem I from Anthocerotibacter panamensis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#10, #2
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)
Molecular weightTheoretical: 86.732508 KDa
SequenceString: MTMTPQGQER PQTRATVDNN PVPTSIEKWG KPGWFERSLA RGPKTTTWIW DLHALAHDFE VQTSDREDIA RKIFAAHFGH LGIVFIWAS IFFFYGALSS NYASWIDNPT GLRPSAQFAI PVFGQEVLND PATAAKGFEQ GGIVMTSGLF HLWRAVGYTN Q TQLLATAV ...String:
MTMTPQGQER PQTRATVDNN PVPTSIEKWG KPGWFERSLA RGPKTTTWIW DLHALAHDFE VQTSDREDIA RKIFAAHFGH LGIVFIWAS IFFFYGALSS NYASWIDNPT GLRPSAQFAI PVFGQEVLND PATAAKGFEQ GGIVMTSGLF HLWRAVGYTN Q TQLLATAV GALVAAGLMF FGGWFHYHVR APKLEWFQNV ESMLNHHLAG LLGLGSLAWT GHLIHVALPV NQMLDKGMKA AD IPLPHEY AFSTEAMGNF FPSFKQGLLP FFTGNWAVYS DFLTFKGGLN PQTGSLWMTD IAHHHLAIAV MFIIAGHMYR TNG PWNPLG LGHSIKEILE AHKGPFTGEG HKGLYEVLTT SWHAQLAINL AMVGSLSIIV AHHMYAMNPY PYMGIDYPTQ ISLF THHMW IGGFLIVGAG AHAAIFMVRD YDPAVNQNNL LDRVLRHRDA IISHLNWVCL FLGFHSFGLY VHNDTMQALG RPGDM FADW GIQLQPVFAQ WIQSVNAAAF GPNSTAPWVS AATSPVWGGN VLALPATVAG EVVQKISIAP VPLGTADFMI HHIHAL TIH VTILILLKGV LFARSSRLIP DKANLGFRFP CDGPGRGGTC QSSAWDHVFL GLFWMYNCIS IVIFHFSWKM QSDVYGT LN ATTKAVEHIV PSTDVLLGNG TTQAFTQFAA SSVNINGWLR DFLWAQAAPV INSYGGPSAA YGLFFLGAHF VWAFSLMF L FSGRGYWQEL IESIVWAHNK LKIVPTIQPR ALSITQGRAV GVAHYLLGGI VTTWAFFIAR FLAI

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Macromolecule #2: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)
Molecular weightTheoretical: 3.319953 KDa
SequenceString:
MLINNFEVAG AFVAALIAGF FALMLSTTLG KS

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Macromolecule #3: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)
Molecular weightTheoretical: 82.935758 KDa
SequenceString: MATRFPKFSQ DLAQDPTTRR IWYGIATAHD FESHDGMTEE TLYQKIFASH FGHIAIIFLW ASSFNFHVAW QGNFEQWLTD PTKVKPIAH AIFDPHFGPG AVKAFTPEGG SGPVNIMYSG LYYFWYTIGI RHNSELYEGA IFLILLAALF LAAGWLHLQP R FRPSLAWF ...String:
MATRFPKFSQ DLAQDPTTRR IWYGIATAHD FESHDGMTEE TLYQKIFASH FGHIAIIFLW ASSFNFHVAW QGNFEQWLTD PTKVKPIAH AIFDPHFGPG AVKAFTPEGG SGPVNIMYSG LYYFWYTIGI RHNSELYEGA IFLILLAALF LAAGWLHLQP R FRPSLAWF KNAESRLNHH LSALFGVSSL AWAGHMVHVA IPRAYGKEVN WSNFLQIAPH DAGLSAFFTG NWGAYAQPGA NG SPPILTF IGGLNPQTGS LPLGDIAHHH LAIAVIFIIA GHMYRTNFGI GHNLKELVDG QVWPGVGAGH RGLYDTVNNS LHF QLSLAL ASLGTVTSLV AQQMYALPPY AFMAKDHTTM AALYTHHQYI AGFLLVGAFA HAAIFWVRDY DPEANKDNVL ARVL AHKEA IISHLSWVSL FLGFHTLGLY VHNDVMQAFG RPEDQILIEP VFAQWVQAQS GVLIPGMAPI FGFLQDNATL GTTPA AAGT FGLGWFCSVN GGPGLTEAAT GILKTCFDNG YGKLETPVFL PIGPGDFLVH HAIALGIHTT VLILVKGALD ARGTKL MPD KKDFGYAFPC DGPGRGGTCD ISAWDAFYLS MFWMLNTLGW ITFYWHWKHL AIWTDNVASF NTNSVYLMGW LRDYLWA YS SPLINGYGPS AAVNNLSVWS WMFLFGHLVW ATGFMFLISW RGYWQELIET LVWAHERTPL ANLVRWKDKP VAMSIVQG R LIGLAHFTVG YILTYAAFVI ASTAGLST

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Macromolecule #4: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)
Molecular weightTheoretical: 8.805158 KDa
SequenceString:
MSHAVKIYDT CIGCTQCVRA CPLDVLEMVP WDGNRAGSIA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

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Macromolecule #5: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)
Molecular weightTheoretical: 15.481709 KDa
SequenceString:
MTQANSLPPG ASSPIFGGST GGLLRKALVE EKYLITWGSK EEQVFEMPTG GAATMVAGVN GLYLARKEQC HALHRQLVAK FKIRDSKIY RVLPNGEQTL IYPKDGVPSE KANPGREVVG YVPRKIGNNP SPISVKFTGG NTYD

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Macromolecule #6: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)
Molecular weightTheoretical: 7.236996 KDa
SequenceString:
MSIQKGSQVR VLRQESYWYN DVGTVASVDK GANVIYPVTV RFEKVNYSNL NTNNFGVSEL EEVS

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Macromolecule #7: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)
Molecular weightTheoretical: 19.575764 KDa
SequenceString:
MKGRMFSWLL GCLMVLCLSP LVLAEPLGNT IPCSESQAFK DLKDARINGL KEKIAATDPA TQYAKDLTAS MELWEYRYAN YEKNASCDK DSGQPHLIVD GRLSHAGDFI IPSILFLWLA GALGWAGRDY LLKTQNAMDE ILIDFSKAVP SLVLGLAWPL F AIPQILSG AIRDNRVKP

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Macromolecule #8: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)
Molecular weightTheoretical: 3.712463 KDa
SequenceString:
MNVYPWLVYV TTLVFPLVSL AALFILIERD TI

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Macromolecule #9: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 9 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)
Molecular weightTheoretical: 4.36439 KDa
SequenceString:
MKIPFLSLAP ISGALFIIGS VVVLALANIY AKYPLLHPLV P

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Macromolecule #10: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 10 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)
Molecular weightTheoretical: 17.047908 KDa
SequenceString:
MQSLSRGMVS TDDFQVGTLL TPVNNSPFIK FFINNLPINR PGLDPFFRGL EVGMAHGYWL FGPFVVLGPL RLTAFRPPDI EQLSILAAL ISAIVVVVAG TLALSLYATV GPDDDTKFGA EGWSRFAGGW LIGGGGGALF AALLYLFRGP LLVMLLGIIP G

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Macromolecule #11: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 11 / Number of copies: 3 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #12: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 12 / Number of copies: 264 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #13: Menaquinone-4

MacromoleculeName: Menaquinone-4 / type: ligand / ID: 13 / Number of copies: 6 / Formula: 1L3
Molecular weightTheoretical: 444.648 Da
Chemical component information

ChemComp-1L3:
Menaquinone-4

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Macromolecule #14: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 14 / Number of copies: 9 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #15: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 15 / Number of copies: 66 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #16: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 16 / Number of copies: 9 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #17: beta,beta-carotene-4,4'-dione

MacromoleculeName: beta,beta-carotene-4,4'-dione / type: ligand / ID: 17 / Number of copies: 3 / Formula: 45D
Molecular weightTheoretical: 564.84 Da
Chemical component information

ChemComp-45D:
beta,beta-carotene-4,4'-dione

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Macromolecule #18: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 18 / Number of copies: 3 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Macromolecule #19: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 19 / Number of copies: 3 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #20: water

MacromoleculeName: water / type: ligand / ID: 20 / Number of copies: 555 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 403080
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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