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- EMDB-54803: Structure of Photosystem I from Chlamydomonas reinhardtii at 1.83... -

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Basic information

Entry
Database: EMDB / ID: EMD-54803
TitleStructure of Photosystem I from Chlamydomonas reinhardtii at 1.83 A resolution
Map dataNon-sharp map
Sample
  • Complex: Photosystem I
    • Protein or peptide: x 18 types
  • Ligand: x 14 types
KeywordsPhotosystem I / Chlamydomonas reinhardtii / CryoEM / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 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 V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Chlorophyll A-B binding protein, plant and chromista ...Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Chlorophyll A-B binding protein, plant and chromista / Photosystem I reaction centre subunit VIII superfamily / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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 PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA / Photosystem I protein PsaC / 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 / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center ...Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.83 Å
AuthorsMahapatra GP / Schuller JM
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structure of Chlamydomonas reinhardtii Photosystem I complexed with cytochrome c.
Authors: Yu Ogawa / Gyana Prakash Mahapatra / Yuval Milrad / Michelle Schimpf / Genji Kurisu / Michael Hippler / Jan Michael Schuller /
Abstract: Photosynthetic electron transfer relies on small soluble carriers that shuttle electrons between the cytochrome b₆f complex and Photosystem I (PSI). While copper-containing plastocyanin (Pc) serves ...Photosynthetic electron transfer relies on small soluble carriers that shuttle electrons between the cytochrome b₆f complex and Photosystem I (PSI). While copper-containing plastocyanin (Pc) serves this role in plants, the heme protein cytochrome c₆ (Cyt c₆) is also employed in algae and cyanobacteria. Here, we present a cryo-electron microscopy structure of a Cyt c₆:PSI complex from Chlamydomonas reinhardtii. We observe that the heme group of Cyt c₆ is positioned ~11 Å away from P700, stabilized by extensive contacts involving a N-terminal helix-loop-helix motif of PSAF, characteristic of eukaryotic PSI. Notably, the algal Cyt c₆ also retains an arginine residue (R66) which is crucial for cyanobacterial donor:PSI reactions. Our structure reveals the previously uncharacterized interactions involving this residue; it can form a putative electrostatic contact with PsaB-D623 while also contributing to a tri-planar π(cation)-π interactions with adjacent residues. Our findings provide a structural framework for understanding the mechanism and evolution of donor:PSI interactions.
History
DepositionAug 15, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54803.png

Downloads & links

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Map

FileDownload / File: emd_54803.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-sharp map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å		0.73 Å/pix.
x 512 pix.
= 373.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.108331144 - 0.3847478
Average (Standard dev.)0.00057170284 (±0.0068816184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54803_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54803_half_map_2.map
Projections & Slices
AxesZYX

Projections

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Photosystem I

EntireName: Photosystem I
Components
  • Complex: Photosystem I
    • Protein or peptide: Light-harvesting chlorophyll-a/b protein of photosystem I, type III
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • 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, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit IV, chloroplastic
    • 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 psaK, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit III, chloroplastic
    • Protein or peptide: Photosystem I reaction center subunit V, chloroplastic
    • Protein or peptide: Chains: L
  • Ligand: CHLOROPHYLL A
  • Ligand: CHLOROPHYLL B
  • Ligand: BETA-CAROTENE
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: PHYLLOQUINONE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: water

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Supramolecule #1: Photosystem I

SupramoleculeName: Photosystem I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Macromolecule #1: Light-harvesting chlorophyll-a/b protein of photosystem I, type III

MacromoleculeName: Light-harvesting chlorophyll-a/b protein of photosystem I, type III
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.888234 KDa
SequenceString: QLYVGASQSS LAYLDGSLPG DFGFDPLGLL DPVNSGGFIE PKWLQYSEVI HARWAMLGAA GCIAPEVLGA AGLIPDATNI KWFESGVIP PAGSYNGYWA DPYTIFFVEI VAMQFAELRR LQDFRYPGSM GQQYFLGLEA IFKGSGDAAY PGGPFFNLFN L GKTEAAMK ...String:
QLYVGASQSS LAYLDGSLPG DFGFDPLGLL DPVNSGGFIE PKWLQYSEVI HARWAMLGAA GCIAPEVLGA AGLIPDATNI KWFESGVIP PAGSYNGYWA DPYTIFFVEI VAMQFAELRR LQDFRYPGSM GQQYFLGLEA IFKGSGDAAY PGGPFFNLFN L GKTEAAMK ELKLKEIKNG RLAMLAMLGY GAQAVMTGKG PFQNLVEHLA DPVNNNILTN FAG

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #2: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.304559 KDa
SequenceString: KRDAALPSWM PGADLPGYLN GTLPGDFGFD PLYLGQDPVK LKWYAQAELM NARFAMLAVA GILVPELLSN IGFSWPGAGV AWYDAGKFE YFAPASSLFG VQMLLFAWVE IRRYQDFVKP GSANQDPIFT NNKLPDGNEP GYPGGIFDPF GWSKGDIKSL K LKEIKNGR ...String:
KRDAALPSWM PGADLPGYLN GTLPGDFGFD PLYLGQDPVK LKWYAQAELM NARFAMLAVA GILVPELLSN IGFSWPGAGV AWYDAGKFE YFAPASSLFG VQMLLFAWVE IRRYQDFVKP GSANQDPIFT NNKLPDGNEP GYPGGIFDPF GWSKGDIKSL K LKEIKNGR LAMLAFAGFI GQAYTTGTTP LKNLSTHLAD PWSTTVWQND LARL

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 25.122805 KDa
SequenceString: DRKLWAPGVV APEYLKGDLA GDYGWDPLGL GADPTALKWY RQSELQHARW AMLGVAGVLV QEIVKPDVYF YEAGLPQNLP EPFTNINMG GLLAWEFILM HWVEVRRWQD YKNFGSVNED PIFKGNKVPN PEMGYPGGIF DPFGFSKGNL KELQTKEIKN G RLAMIAYM ...String:
DRKLWAPGVV APEYLKGDLA GDYGWDPLGL GADPTALKWY RQSELQHARW AMLGVAGVLV QEIVKPDVYF YEAGLPQNLP EPFTNINMG GLLAWEFILM HWVEVRRWQD YKNFGSVNED PIFKGNKVPN PEMGYPGGIF DPFGFSKGNL KELQTKEIKN G RLAMIAYM AFILQAQATG KGPLAALSAH LSNPFGNNIL KNIGTCTVPH SVDVQGLTIP LTCLWPGSQ

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #4: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 25.025 KDa
SequenceString: SRPLWLPGST PPAHLKGDLP GDFGFDPLGL GANAESLKWF KESELVHSRW AMAAVAGILV QEIVRPDVFW YNAGKEVESP LGPLGLLAV EFFLMHWVEV RRWQDLRKPG SVDQDPIFSQ YKLPPHEVGY PGGVFAPFIP GDLAELKVKE IKNGRLAMLA F VGFVMAAQ ...String:
SRPLWLPGST PPAHLKGDLP GDFGFDPLGL GANAESLKWF KESELVHSRW AMAAVAGILV QEIVRPDVFW YNAGKEVESP LGPLGLLAV EFFLMHWVEV RRWQDLRKPG SVDQDPIFSQ YKLPPHEVGY PGGVFAPFIP GDLAELKVKE IKNGRLAMLA F VGFVMAAQ VTGKGPIAAL QEHLADPWGT TIFSKAAVVP GQAVAPPCKI PASVSYKGIE IPTPCFLQGL WP

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #5: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.304396 KDa
SequenceString: VRPVWFPGNP PPAHLDGSLA GDYGFDPLFL GQEPQTLKWY VQAELVHGRF AMLGAAGIIL TSIGAKVGLG FPEWYDAGKV VVEKNNIDF PTLMVIQFYL MGWAETKRWY DFKNPGSQAD GSFLGFTEEF KGLENGYPGG RFFDPMGLSR GDAAKYQEYK Q KEVKNGRL ...String:
VRPVWFPGNP PPAHLDGSLA GDYGFDPLFL GQEPQTLKWY VQAELVHGRF AMLGAAGIIL TSIGAKVGLG FPEWYDAGKV VVEKNNIDF PTLMVIQFYL MGWAETKRWY DFKNPGSQAD GSFLGFTEEF KGLENGYPGG RFFDPMGLSR GDAAKYQEYK Q KEVKNGRL AMIACLGFAA QYAATGKGPL DNLADHLADP NHVNFATNGV SIPIA

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #6: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.293613 KDa
SequenceString: RQSWLPGSQI PAHLDTPAAQ ALAGNFGFDP LGLGKDPVAL RWYQQAELIH CRTAMAGVAG ILIPGLLTKA GALNVPEWYD AGKVAIENS FAPWGSLLAV QLFLCGFVEA KRWQDIRKPG SQGEPGSFLG FEASLKGTSE LGYPGGPFDP LGLSKEADKW A DWKLKEVK ...String:
RQSWLPGSQI PAHLDTPAAQ ALAGNFGFDP LGLGKDPVAL RWYQQAELIH CRTAMAGVAG ILIPGLLTKA GALNVPEWYD AGKVAIENS FAPWGSLLAV QLFLCGFVEA KRWQDIRKPG SQGEPGSFLG FEASLKGTSE LGYPGGPFDP LGLSKEADKW A DWKLKEVK NGRLAMLAFL GFVAQKYATG AGPVDNLAAH LKDPWHVNYA TNGVSLPFL

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #7: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 82.193023 KDa
SequenceString: AKKVKIAVDR NPVETSFEKW AKPGHFSRTL SKGPNTTTWI WNLHADAHDF DSHTSDLEEI SRKVFSAHFG QLGIIFIWLS GMYFHGARF SNYEAWLSDP THIKPSAQVV WPIVGQEILN GDVGGGFQGI QITSGFFQLW RASGITSELQ LYTTAIGGLV M AAAMFFAG ...String:
AKKVKIAVDR NPVETSFEKW AKPGHFSRTL SKGPNTTTWI WNLHADAHDF DSHTSDLEEI SRKVFSAHFG QLGIIFIWLS GMYFHGARF SNYEAWLSDP THIKPSAQVV WPIVGQEILN GDVGGGFQGI QITSGFFQLW RASGITSELQ LYTTAIGGLV M AAAMFFAG WFHYHKAAPK LEWFQNVESM LNHHLGGLLG LGSLAWAGHQ IHVSLPVNKL LDAGVDPKEI PLPHDLLLNR AI MADLYPS FAKGIAPFFT LNWSEYSDFL TFKGGLNPVT GGLWLSDTAH HHVAIAVLFL VAGHMYRTNW GIGHSMKEIL EAH RGPFTG EGHVGLYEIL TTSWHAQLAI NLALFGSLSI IVAHHMYAMP PYPYLATDYG TQLSLFTHHT WIGGFCIVGA GAHA AIFMV RDYDPTNNYN NLLDRVIRHR DAIISHLNWV CIFLGFHSFG LYIHNDTMSA LGRPQDMFSD TAIQLQPVFA QWIQN THFL APQLTAPNAL AATSLTWGGD LVAVGGKVAM MPISLGTSDF MVHHIHAFTI HVTVLILLKG VLFARSSRLI PDKANL GFR FPCDGPGRGG TCQVSAWDHV FLGLFWMYNS LSIVIFHFSW KMQSDVWGTV TASGVSHITG GNFAQSANTI NGWLRDF LW AQSSQVIQSY GSALSAYGLI FLGAHFVWAF SLMFLFSGRG YWQELIESIV WAHNKLKVAP AIQPRALSIT QGRAVGVA H YLLGGIATTW SFFLARIISV G

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A1

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Macromolecule #8: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 81.981992 KDa
SequenceString: TKLFPKFSQG LAQDPTTRRI WYGLAMAHDF ESHDGMTEEN LYQKIFASHF GQLSIIFLWT SGNLFHVAWQ GNFEQWVTDP VHIRPIAHA IWDPHFGQPA VEAFTRGGAS GPVNISTSGV YQWWYTIGMR TNQDLYVGSV FLALVSAIFL FAGWLHLQPN F QPSLSWFK ...String:
TKLFPKFSQG LAQDPTTRRI WYGLAMAHDF ESHDGMTEEN LYQKIFASHF GQLSIIFLWT SGNLFHVAWQ GNFEQWVTDP VHIRPIAHA IWDPHFGQPA VEAFTRGGAS GPVNISTSGV YQWWYTIGMR TNQDLYVGSV FLALVSAIFL FAGWLHLQPN F QPSLSWFK DAESRLNHHL SGLFGVSSLA WTGHLVHVAI PESRGQHVGW DNFLSVLPHP QGLTPFFTGN WAAYAQSPDT AS HVFGTAQ GSGQAILTFL GGFHPQTQSL WLTDMAHHHL AIAVIFIVAG HMYRTNFGIG HRMQAILEAH TPPSGSLGAG HKG LFDTVN NSLHFQLGLA LASVGTITSL VAQHMYSLPP YAFQAIDFTT QAALYTHHQY IAGFIMCGAF AHGAIFFIRD YDPE QNKGN VLARMLDHKE ALISHLSWVS LFLGFHTLGL YVHNDVMQAF GTPEKQILIE PVFAQWIQAA HGKALYGFDF LLSSK TSAA FANGQSLWLP GWLDAINNNQ NSLFLTIGPG DFLVHHAIAL GLHTTTLILV KGALDARGSK LMPDKKDFGY SFPCDG PGR GGTCDISAYD AFYLAVFWML NTIGWVTFYW HWKHLTLWQG NVAQFDESST YLMGWLRDYL WLNSSQLING YNPFGMN SL SVWAWTFLFG HLIYATGFMF LISWRGYWQE LIETLVWAHE KTPLANLVYW KDKPVALSIV QARLVGLAHF SVGYIFTY A AFLIASTSGR FG

UniProtKB: Photosystem I P700 chlorophyll a apoprotein A2

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Macromolecule #9: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 8.73813 KDa
SequenceString:
AHIVKIYDTC IGCTQCVRAC PLDVLEMVPW DGCKASQMAS APRTEDCVGC KRCETACPTD FLSVRVYLGS ESTRSMGLSY

UniProtKB: Photosystem I iron-sulfur center

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Macromolecule #10: Photosystem I reaction center subunit II, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit II, chloroplastic
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 16.123686 KDa
SequenceString:
WTVPTLNPDT PSPIFGGSTG GLLRKAQTEE FYVITWEAKK EQIFEMPTGG AAIMRQGPNL LKFGKKEQCL ALTTQLRNKF KLTPCFYRV FPDGKVQYLH PADGVYPEKV NAGRVGANQN MRRIGQNVNP IKVKFSGRMM SPAEI

UniProtKB: Photosystem I reaction center subunit II, chloroplastic

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Macromolecule #11: Photosystem I reaction center subunit IV, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit IV, chloroplastic
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 7.151057 KDa
SequenceString:
EVGPKRGSLV KILRPESYWF NQVGKVVSVD QSGVRYPVVV RFENQNYAGV TTNNYALDEV VAAK

UniProtKB: Photosystem I reaction center subunit IV, chloroplastic

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Macromolecule #12: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.970731 KDa
SequenceString:
PFVPPSWAPS VFVPLTGLVL PAIAMATLFV YIEKEAP

UniProtKB: Photosystem I reaction center subunit VIII

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Macromolecule #13: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.629373 KDa
SequenceString:
(ACE)MKDFTTYLS TAPVIATIWF TFTAGLLIEI NRYFPDPLVF S

UniProtKB: Photosystem I reaction center subunit IX

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Macromolecule #14: Photosystem I reaction center subunit psaK, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit psaK, chloroplastic
type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 8.316676 KDa
SequenceString:
GFIGSSTNLI MVASTTATLA AARFGLAPTV KKNTTAGLKL VDSKNSAGVI SNDPAGFTIV DVLAMGAAGH GLGVGIVLGL KGIGAL

UniProtKB: Photosystem I reaction center subunit psaK, chloroplastic

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Macromolecule #15: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 20.368023 KDa
SequenceString: KAGNWLPGSD APAWLPDDLP GNYGFDPLSL GKEPASLKRF TESEVIHGRW AMLGVAGSLA VELLGYGNWY DAPLWAVNGG KATWFGIEV PFDLNALLAF EFVAMAAAEG QRGDAGGVVY PGGAFDPLGF AKDSSKSGEL KLKEIKNGRL AMVAFLGFVA Q HAATGKGP ...String:
KAGNWLPGSD APAWLPDDLP GNYGFDPLSL GKEPASLKRF TESEVIHGRW AMLGVAGSLA VELLGYGNWY DAPLWAVNGG KATWFGIEV PFDLNALLAF EFVAMAAAEG QRGDAGGVVY PGGAFDPLGF AKDSSKSGEL KLKEIKNGRL AMVAFLGFVA Q HAATGKGP IAALGEHLAN PWGANFATNG ISVPFF

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #16: Photosystem I reaction center subunit III, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit III, chloroplastic
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 17.957773 KDa
SequenceString:
DIAGLTPCSE SKAYAKLEKK ELKTLEKRLK QYEADSAPAV ALKATMERTK ARFANYAKAG LLCGNDGLPH LIADPGLALK YGHAGEVFI PTFGFLYVAG YIGYVGRQYL IAVKGEAKPT DKEIIIDVPL ATKLAWQGAG WPLAAVQELQ RGTLLEKEEN I TVSPR

UniProtKB: Photosystem I reaction center subunit III, chloroplastic

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Macromolecule #17: Photosystem I reaction center subunit V, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit V, chloroplastic
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 9.958093 KDa
SequenceString:
LDPQIVISGS TAAFLAIGRF VFLGYQRREA NFDSTVGPKT TGATYFDDLQ KNSTIFATND PAGFNIIDVA GWGALGHAVG FAVLAINSL QGANLS

UniProtKB: Photosystem I reaction center subunit V, chloroplastic

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Macromolecule #18: Chains: L

MacromoleculeName: Chains: L / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 12.744637 KDa
SequenceString:
GMLETPVTSA PIVATYLSNL PAYRTGVAPV LRGVEIGLAH GFLLAGPFIK LGPLRNVPET AEIAGSLSAA GLVLILALCL SIYGSAQFQ SARDPLFSAD GWSEFAAGFL VGGEAGVAWA YVCTQ

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Macromolecule #19: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 19 / Number of copies: 188 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #20: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 20 / Number of copies: 28 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #21: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 21 / Number of copies: 27 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #22: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 22 / Number of copies: 16 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #23: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 23 / Number of copies: 12 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #24: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 24 / Number of copies: 27 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMU:
DODECYL-ALPHA-D-MALTOSIDE / detergent*YM

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Macromolecule #25: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 25 / Number of copies: 7 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-XAT:
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 26 / Number of copies: 14 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #27: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
type: ligand / ID: 27 / Number of copies: 2 / Formula: NEX
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-NEX:
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL

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Macromolecule #28: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 28 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

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Macromolecule #29: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 29 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #30: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 30 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #31: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 31 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #32: water

MacromoleculeName: water / type: ligand / ID: 32 / Number of copies: 1019 / 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

Concentration1.5 mg/mL
BufferpH: 7.5 / Details: 5mM HEPES, pH 7.5, 0.02% alphaDDM
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 4 / Average exposure time: 1.9 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 30
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 246159
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.7.1)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7zqc


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9se6:
Structure of Photosystem I from Chlamydomonas reinhardtii at 1.83 A resolution

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