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- EMDB-12697: Structure of a Minimal Photosystem I -

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Basic information

Entry
Database: EMDB / ID: EMD-12697
TitleStructure of a Minimal Photosystem I
Map data
Sample
  • Complex: Minimal Photosystem I
    • Protein or peptide: x 7 types
  • Ligand: x 8 types
Function / homology
Function and homology information


plasma membrane-derived photosystem I / 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 ...plasma membrane-derived photosystem I / 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 reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaD ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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 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 reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit PsaK 2
Similarity search - Component
Biological speciesSynechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.31 Å
AuthorsNelson N / Caspy I / Lambrev P
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
CitationJournal: J Am Chem Soc / Year: 2021
Title: Two-Dimensional Electronic Spectroscopy of a Minimal Photosystem I Complex Reveals the Rate of Primary Charge Separation.
Authors: Parveen Akhtar / Ido Caspy / Paweł J Nowakowski / Tirupathi Malavath / Nathan Nelson / Howe-Siang Tan / Petar H Lambrev /
Abstract: Photosystem I (PSI), found in all oxygenic photosynthetic organisms, uses solar energy to drive electron transport with nearly 100% quantum efficiency, thanks to fast energy transfer among antenna ...Photosystem I (PSI), found in all oxygenic photosynthetic organisms, uses solar energy to drive electron transport with nearly 100% quantum efficiency, thanks to fast energy transfer among antenna chlorophylls and charge separation in the reaction center. There is no complete consensus regarding the kinetics of the elementary steps involved in the overall trapping, especially the rate of primary charge separation. In this work, we employed two-dimensional coherent electronic spectroscopy to follow the dynamics of energy and electron transfer in a monomeric PSI complex from PCC 6803, containing only subunits A-E, K, and M, at 77 K. We also determined the structure of the complex to 4.3 Å resolution by cryoelectron microscopy with refinements to 2.5 Å. We applied structure-based modeling using a combined Redfield-Förster theory to compute the excitation dynamics. The absorptive 2D electronic spectra revealed fast excitonic/vibronic relaxation on time scales of 50-100 fs from the high-energy side of the absorption spectrum. Antenna excitations were funneled within 1 ps to a small pool of chlorophylls absorbing around 687 nm, thereafter decaying with 4-20 ps lifetimes, independently of excitation wavelength. Redfield-Förster energy transfer computations showed that the kinetics is limited by transfer from these red-shifted pigments. The rate of primary charge separation, upon direct excitation of the reaction center, was determined to be 1.2-1.5 ps. This result implies activationless electron transfer in PSI.
History
DepositionMar 30, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateSep 22, 2021-
Current statusSep 22, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7o1v
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12697.png

Downloads & links

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Map

FileDownload / File: emd_12697.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8328 Å
Density
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.011
Minimum - Maximum-0.033085555 - 0.088419944
Average (Standard dev.)9.346269e-05 (±0.0028571703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 233.18399 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.83280.83280.8328
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z233.184233.184233.184
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ640640640
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0330.0880.000

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Supplemental data

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Sample components

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Entire : Minimal Photosystem I

EntireName: Minimal Photosystem I
Components
  • Complex: Minimal Photosystem I
    • 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 PsaK 2
    • Protein or peptide: Photosystem I reaction center subunit XII
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: beta,beta-caroten-4-one
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

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Supramolecule #1: Minimal Photosystem I

SupramoleculeName: Minimal Photosystem I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (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: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 81.722875 KDa
SequenceString: KVSVDNNPVP TSFEKWGKPG HFDRTLARGP KTTTWIWNLH ANAHDFDSQT SDLEDVSRKI FSAHFGHLAV VFVWLSGMYF HGAKFSNYE GWLADPTHIK PSAQVVWPIV GQGILNGDVG GGFHGIQITS GLFYLWRASG FTDSYQLYCT AIGGLVMAAL M LFAGWFHY ...String:
KVSVDNNPVP TSFEKWGKPG HFDRTLARGP KTTTWIWNLH ANAHDFDSQT SDLEDVSRKI FSAHFGHLAV VFVWLSGMYF HGAKFSNYE GWLADPTHIK PSAQVVWPIV GQGILNGDVG GGFHGIQITS GLFYLWRASG FTDSYQLYCT AIGGLVMAAL M LFAGWFHY HVKAPKLEWF QNVESMMNHH LAGLLGLGSL GWAGHQIHVS MPINKLLDAG VAPKDIPLPH EFILEPSKMA EL YPSFAQG LTPFFTLNWG VYSDFLTFKG GLNPVTGGLW LSDTAHHHLA IAVLFIIAGH MYRTNWGIGH SMKEILEAHK GPF TGEGHK GLYEILTTSW HAQLAINLAL LGSLTIIVAQ HMYAMPPYPY QAIDYATQLS LFTHHMWIGG FLIVGAGAHG AIFM VRDYD PAKNVNNLLD RMLRHRDAII SHLNWVCIFL GFHSFGLYIH NDTMRALGRP QDMFSDTAIQ LQPIFAQWVQ HLHTL APGA TAPNALATAS YAFGGETIAV AGKVAMMPIT LGTADFMVHH IHAFTIHVTA LILLKGVLYA RSSRLVPDKA NLGFRF PCD GPGRGGTCQV SGWDHVFLGL FWMYNSLSIV IFHFSWKMQS DVWGTVSPDG SVTHVTLGNF AQSAITINGW LRDFLWA QA ANVINSYGSA LSAYGIMFLA GHFVFAFSLM FLFSGRGYWQ ELIESIVWAH NKLNVAPAIQ PRALSIIQGR AVGVAHYL L GGIVTTWAFF LARSLSIG

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 81.167258 KDa
SequenceString: TKFPKFSQDL AQDPTTRRIW YGIATAHDFE THDGMTEENL YQKIFASHFG HIAIIFLWTS GTLFHVAWQG NFEQWIKDPL NIRPIAHAI WDPHFGEGAV NAFTQAGASN PVNIAYSGVY HWFYTIGMTT NQELYSGAVF LLVLASLFLF AGWLHLQPKF R PSLAWFKN ...String:
TKFPKFSQDL AQDPTTRRIW YGIATAHDFE THDGMTEENL YQKIFASHFG HIAIIFLWTS GTLFHVAWQG NFEQWIKDPL NIRPIAHAI WDPHFGEGAV NAFTQAGASN PVNIAYSGVY HWFYTIGMTT NQELYSGAVF LLVLASLFLF AGWLHLQPKF R PSLAWFKN AESRLNHHLA GLFGVSSLAW AGHLVHVAIP EARGQHVGWD NFLSTPPHPA GLMPFFTGNW GVYAADPDTA GH IFGTSEG AGTAILTFLG GFHPQTESLW LTDIAHHHLA IAVIFIIAGH MYRTNWGIGH SIKEILNAHK GPLTGAGHTN LYD TINNSL HFQLGLALAS LGVITSLVAQ HMYSLPSYAF IAQDHTTQAA LYTHHQYIAG FLMVGAFAHG AIFFVRDYDP VANK DNVLA RMLEHKEALI SHLSWVSLFL GFHTLGLYVH NDVVVAFGTP EKQILIEPVF AQWIQATSGK ALYGFDVLLS NPDSI ASTT GAAWLPGWLD AINSGTNSLF LTIGPGDFLV HHAIALGLHT TALILIKGAL DARGSKLMPD KKDFGYSFPC DGPGRG GTC DISAWDAFYL AMFWMLNTLG WLTFYWHWKH LGVWSGNVAQ FNENSTYLMG WFRDYLWANS AQLINGYNPY GVNNLSV WA WMFLFGHLVW ATGFMFLISW RGYWQELIET IVWAHERTPL ANLVRWKDKP VALSIVQARL VGLAHFTVGY VLTYAAFL I ASTAGKFG

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 8.706064 KDa
SequenceString:
SHSVKIYDTC IGCTQCVRAC PLDVLEMVPW DGCKAAQIAS SPRTEDCVGC KRCETACPTD FLSIRVYLGA ETTRSMGLAY

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Macromolecule #4: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 15.663749 KDa
SequenceString:
MTELSGQPPK FGGSTGGLLS KANREEKYAI TWTSASEQVF EMPTGGAAIM NEGENLLYLA RKEQCLALGT QLRTKFKPKI QDYKIYRVY PSGEVQYLHP ADGVFPEKVN EGREAQGTKT RRIGQNPEPV TIKFSGKAPY EV

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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: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 7.680478 KDa
SequenceString:
ALNRGDKVRI KRTESYWYGD VGTVASVEKS GILYPVIVRF DRVNYNGFSG SASGVNTNNF AENELELVQ

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Macromolecule #6: Photosystem I reaction center subunit PsaK 2

MacromoleculeName: Photosystem I reaction center subunit PsaK 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 8.237783 KDa
SequenceString:
LAQASPTTAG WSLSVGIIMC LCNVFAFVIG YFAIQKTGKG KDLALPQLAS KKTFGLPELL ATMSFGHILG AGMVLGLASS

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Macromolecule #7: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 3.382063 KDa
SequenceString:
MALSDTQILA ALVVALLPAF LAFRLSTELY K

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Macromolecule #8: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 8 / Number of copies: 88 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #9: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 9 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #10: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 10 / Number of copies: 15 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #11: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 11 / Number of copies: 5 / 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 #12: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 12 / Number of copies: 4 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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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: beta,beta-caroten-4-one

MacromoleculeName: beta,beta-caroten-4-one / type: ligand / ID: 14 / Number of copies: 2 / Formula: ECH
Molecular weightTheoretical: 550.856 Da
Chemical component information

ChemComp-ECH:
beta,beta-caroten-4-one / Echinenone

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Macromolecule #15: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 15 / Number of copies: 1 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

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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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 2493 / Average electron dose: 43.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 286538
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5oy0

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74303
FSC plot (resolution estimation)

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