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- EMDB-30882: Photosystem I from a chlorophyll d-containing cyanobacterium Acar... -

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Basic information

Entry
Database: EMDB / ID: EMD-30882
TitlePhotosystem I from a chlorophyll d-containing cyanobacterium Acaryochloris marina
Map data
Sample
  • Complex: Photosystem I from a chlorophyll d-containing cyanobacterium Acaryochloris marina
    • Protein or peptide: x 10 types
  • Ligand: x 8 types
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
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 PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily ...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 PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / 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 / 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
Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit II / Photosystem I iron-sulfur center
Similarity search - Component
Biological speciesAcaryochloris marina MBIC11017 (bacteria) / Acaryochloris marinan MBIC11017 (bacteria) / Acaryochloris marina MBIC 11017 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen JH / Zhang X / Shen JR
CitationJournal: J Integr Plant Biol / Year: 2021
Title: A unique photosystem I reaction center from a chlorophyll d-containing cyanobacterium Acaryochloris marina.
Authors: Caihuang Xu / Qingjun Zhu / Jing-Hua Chen / Liangliang Shen / Xiaohan Yi / Zihui Huang / Wenda Wang / Min Chen / Tingyun Kuang / Jian-Ren Shen / Xing Zhang / Guangye Han /
Abstract: Photosystem I (PSI) is a large protein supercomplex that catalyzes the light-dependent oxidation of plastocyanin (or cytochrome c ) and the reduction of ferredoxin. This catalytic reaction is ...Photosystem I (PSI) is a large protein supercomplex that catalyzes the light-dependent oxidation of plastocyanin (or cytochrome c ) and the reduction of ferredoxin. This catalytic reaction is realized by a transmembrane electron transfer chain consisting of primary electron donor (a special chlorophyll (Chl) pair) and electron acceptors A , A , and three Fe S clusters, F , F , and F . Here we report the PSI structure from a Chl d-dominated cyanobacterium Acaryochloris marina at 3.3 Å resolution obtained by single-particle cryo-electron microscopy. The A. marina PSI exists as a trimer with three identical monomers. Surprisingly, the structure reveals a unique composition of electron transfer chain in which the primary electron acceptor A is composed of two pheophytin a rather than Chl a found in any other well-known PSI structures. A novel subunit Psa27 is observed in the A. marina PSI structure. In addition, 77 Chls, 13 α-carotenes, two phylloquinones, three Fe-S clusters, two phosphatidyl glycerols, and one monogalactosyl-diglyceride were identified in each PSI monomer. Our results provide a structural basis for deciphering the mechanism of photosynthesis in a PSI complex with Chl d as the dominating pigments and absorbing far-red light.
History
DepositionJan 17, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dwq
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7dwq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30882.png

Downloads & links

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Map

FileDownload / File: emd_30882.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.307 Å
Density
Contour LevelBy AUTHOR: 0.171 / Movie #1: 0.6
Minimum - Maximum-1.735202 - 5.061297
Average (Standard dev.)-0.0012252178 (±0.07993085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 522.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3071.3071.307
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z522.800522.800522.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.7355.061-0.001

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Supplemental data

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Sample components

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Entire : Photosystem I from a chlorophyll d-containing cyanobacterium Acar...

EntireName: Photosystem I from a chlorophyll d-containing cyanobacterium Acaryochloris marina
Components
  • Complex: Photosystem I from a chlorophyll d-containing cyanobacterium Acaryochloris marina
    • Protein or peptide: Photosystem I protein PsaD
    • Protein or peptide: Photosystem I P740 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P740 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I protein PsaF
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I protein PsaL
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Photosystem I protein Psa27
  • Ligand: CHLOROPHYLL D
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: CHLOROPHYLL D ISOMER
  • Ligand: PHEOPHYTIN APheophytin
  • Ligand: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Supramolecule #1: Photosystem I from a chlorophyll d-containing cyanobacterium Acar...

SupramoleculeName: Photosystem I from a chlorophyll d-containing cyanobacterium Acaryochloris marina
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)

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Macromolecule #1: Photosystem I protein PsaD

MacromoleculeName: Photosystem I protein PsaD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 15.114146 KDa
SequenceString:
MAETLTGQTP LFGGSTGGLL SSAETEEKYA ITWTSPKQQV FEMPTGGAAV MNEGENLLYL ARKEQCLALG LRQLRTKKIM DYKIYRVLP DGSNTLLHPK DGVFPEKSNE GRAAVNSVAR SIGENPNPGA IKYTGKKAYD

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Macromolecule #2: Photosystem I P740 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P740 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 83.470539 KDa
SequenceString: MTTSPGGPET KGRTAEVDIN PVSASLEVAG KPGHFNKSLS KGPQTTTWIW NLHALAHDFD TQTNDLEEIS RKIFSAHFGH LSIIFVWIS GMIFHAARFS NYYAWLADPL GNKPSAHVVW PIVGQDILNA DVGNGFRGVQ ITSGLFHILR GAGMTDPGEL Y SAAIGALV ...String:
MTTSPGGPET KGRTAEVDIN PVSASLEVAG KPGHFNKSLS KGPQTTTWIW NLHALAHDFD TQTNDLEEIS RKIFSAHFGH LSIIFVWIS GMIFHAARFS NYYAWLADPL GNKPSAHVVW PIVGQDILNA DVGNGFRGVQ ITSGLFHILR GAGMTDPGEL Y SAAIGALV AAVVMMYAGY YHYHKKAPKL EWFQNAESTM THHLIVLLGL GNLAWTGHLI HVSLPVNKLL DSGVAPQDIP IP HEFLFDN GFMADLYPSF AQGLMPYFTL NWGAYSDFLT FKGGLDPTTG GLWMTDIAHH HLALAVMYII AGHMYRTNWG IGH SMKEIM ESHKGPFTGE GHKGLYEVLT TSWHAQLAIN LATWGSFSII VAHHMYAMPP YPYLATDYGT QLNLFVHHMW IGGF LIVGG AAHAAIFMVR DYDPAVNQNN VLDRMLRHRD TIISHLNWVC IFLGFHSFGL YIHNDNMRSL GRPQDMFSDT AIQLQ PIFS QWVQNLQANV AGTIRAPLAE GASSLAWGGD PLFVGGKVAM QHVSLGTADF MIHHIHAFQI HVTVLILIKG VLYARS SRL IPDKANLGFR FPCDGPGRGG TCQSSGWDHI FLGLFWMYNC ISIVNFHFFW KMQSDVWGAA NANGGVNYLT AGNWAQS SI TINGWLRDFL WAQSVQVINS YGSALSAYGI LFLGAHFIWA FSLMFLFSGR GYWQELIESI VWAHSKLKIA PAIQPRAM S ITQGRAVGLG HYLLGGIVTS WSFYLARILA LG

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Macromolecule #3: Photosystem I P740 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P740 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 82.210555 KDa
SequenceString: MATKFPSFSQ DLAQDPTTRR IWYGIATVHD FETHDGMTEE NLYQKIFATH FGHLSIIFLW SAGHLFHVAW QGNFEQWIQD PLTIRPIAH AIWDPHLGDA ATQAFTQAGA SGPVDLCYSG LYQWWYTIGM RTNGDLYIGS VFLMIVAAVM LFAGWLHLQP K FRPSLAWF ...String:
MATKFPSFSQ DLAQDPTTRR IWYGIATVHD FETHDGMTEE NLYQKIFATH FGHLSIIFLW SAGHLFHVAW QGNFEQWIQD PLTIRPIAH AIWDPHLGDA ATQAFTQAGA SGPVDLCYSG LYQWWYTIGM RTNGDLYIGS VFLMIVAAVM LFAGWLHLQP K FRPSLAWF RDAESQMNHH LAVLFGASSL GWTGHLIHVA IPEARGQHVG WDNFLSTMPH PAGLAPFFTG RWGVYAQNPD TA GHIFGTS EGAGTAIITF IGGFHPQTEA LWLTDIAHHH LAIAVMYIIA GHMYRTQFGI GHSMKEILEA HTPPSGMLGD AHK GLYDTY NESLHFQLGF HLAALGVITS VVAQHMYSLP SYAFISQDHV TQAALYTHHQ YIAGILAIGA FAHGGIFFVR DYDP ERNKN NVLARALEHK EAIISHLSWV SMFSGFHTLG VYVHNDTVVA FGTPEKQILV EPIFAQWIQA AHGKLLLGFE TLLSN PNGL AYNPPNISPD VFVPGWVEAM NNPVIGPFMS QGPGDFLVHH GIAFSLHVTV LICVKGCLDA RGSKLMPDKK DFGYSF PCD GPGRGGTCDI SAWDSFYLAF FWMLNTIGWI VFYFNWKHLA IWSGNEAQFN TNSTYLMGWL RDYLWGYSAQ LINGYTP FG VNSLSVWAWI FLLGHLCWAT GFLFLISWRG YWQELIETLV WAHQRTPLAN LVTWKDKPVA LSIVQGRLVG LVHFAVGY Y VTYAAFVIGA TAPLG

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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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Acaryochloris marinan MBIC11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 8.825207 KDa
SequenceString:
MSHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKAGQIA SSPRTEDCVG CKRCETACPT DFLSIRVYLG AETTRSMGLA Y

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Macromolecule #5: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 9.560822 KDa
SequenceString:
MVQRGSKVRI LRPESYWFRE IGTVASVDQS GIKYPVIVRF DTCNYNGISG TAAGINTNNF GVHELEEVEA PKGGKKPAAK PAAAPKAEG

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Macromolecule #6: Photosystem I protein PsaF

MacromoleculeName: Photosystem I protein PsaF / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 17.844621 KDa
SequenceString:
MRRLFAVLLV MTLFLGVVPP ASADIGGLVP CSESPKFQER AAKARNTTAD PNSGQKRFEM YSSALCGPED GLPRIIAGGP MRRAGDFLI PGLFFIYIAG GIGNSSRNYQ IANRKKNAKN PAMGEIIIDV PLAVSSTIAG MAWPLTAFRE LTSGELTVPD S DVTVSPR

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Macromolecule #7: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC 11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 5.900939 KDa
SequenceString:
MGDVPLKIDS EKDFMKFFST APVIALVFFT LTAGFLVELN RFFPDILFFP Y

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Macromolecule #8: Photosystem I protein PsaL

MacromoleculeName: Photosystem I protein PsaL / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC 11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 15.349588 KDa
SequenceString:
MTMDLVKHGG DPLVGDLATP VNSSGIVKAW INNLPAYRKG MSANARGLEI GMAHGYYLYG PFATSGPIRG TTMSLVSGVL SASAVVIVL SVAIQIYSSV SSAKPLPSVT TADPGSDFGT KEGWSAVGSG FLIGGCGGAV IAGVLSYAIA AFVG

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Macromolecule #9: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 3.190899 KDa
SequenceString:
MELSDLQIVI ALVVALLPAL LALNLGSALS K

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Macromolecule #10: Photosystem I protein Psa27

MacromoleculeName: Photosystem I protein Psa27 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017
Molecular weightTheoretical: 3.648337 KDa
SequenceString:
MISDILPAIM TPLVVLIGGG AAMTAFFYYV EREG

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Macromolecule #11: CHLOROPHYLL D

MacromoleculeName: CHLOROPHYLL D / type: ligand / ID: 11 / Number of copies: 76 / Formula: CL7
Molecular weightTheoretical: 895.462 Da
Chemical component information

ChemComp-CL7:
CHLOROPHYLL D / Chlorophyll d

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Macromolecule #12: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 12 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #13: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 13 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #14: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

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

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

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Macromolecule #15: CHLOROPHYLL D ISOMER

MacromoleculeName: CHLOROPHYLL D ISOMER / type: ligand / ID: 15 / Number of copies: 1 / Formula: G9R
Molecular weightTheoretical: 895.462 Da
Chemical component information

ChemComp-G9R:
CHLOROPHYLL D ISOMER

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Macromolecule #16: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 16 / Number of copies: 2 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A / Pheophytin

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Macromolecule #17: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta...

MacromoleculeName: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
type: ligand / ID: 17 / Number of copies: 13 / Formula: 8CT
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-8CT:
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene

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

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

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

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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
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 2.5 µm / Calibrated magnification: 38244 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-40 / Average exposure time: 10.0 sec. / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1523356 / Details: raw particles
Initial angle assignmentType: OTHER
Final 3D classificationNumber classes: 3 / Avg.num./class: 129823 / Software - Name: cryoSPARC (ver. 2.12)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.12)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Number images used: 240880

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