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- PDB-6zzx: Structure of low-light grown Chlorella ohadii Photosystem I -

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Basic information

Entry
Database: PDB / ID: 6zzx
TitleStructure of low-light grown Chlorella ohadii Photosystem I
Components
  • (Chlorophyll a-b binding protein, ...Light-harvesting complexes of green plants) x 6
  • (Photosystem I ...) x 13
  • Glutathione reductase
  • Lhca4
  • Lhca7
  • PSI-F
KeywordsPHOTOSYNTHESIS / photosystem I / light stress
Function / homology
Function and homology information


malate transport / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / acyltransferase activity, transferring groups other than amino-acyl groups ...malate transport / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / acyltransferase activity, transferring groups other than amino-acyl groups / chlorophyll binding / chloroplast thylakoid membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / photosynthesis / cell redox homeostasis / monooxygenase activity / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / protein kinase activity / iron ion binding / protein phosphorylation / heme binding / magnesium ion binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Protein of unknown function DUF3067 / Domain of unknown function (DUF3067) / Aluminum-activated malate transporter / Aluminium activated malate transporter / Photosystem I PsaO / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily ...Protein of unknown function DUF3067 / Domain of unknown function (DUF3067) / Aluminum-activated malate transporter / Aluminium activated malate transporter / Photosystem I PsaO / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / 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 reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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 reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / 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 / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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 / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Electron transport accessory-like domain superfamily / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / Acetyltransferase (GNAT) family / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Gcn5-related N-acetyltransferase (GNAT) domain profile. / 4Fe-4S dicluster domain / GNAT domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Acyl-CoA N-acyltransferase / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Leucine-rich repeat domain superfamily / FAD/NAD(P)-binding domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
benzene-1,3,5-triol / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Tripalmitoylglycerol / ASTAXANTHIN / BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) ...benzene-1,3,5-triol / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Tripalmitoylglycerol / ASTAXANTHIN / BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / beta,beta-caroten-4-one / Chem-LAP / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LPX / Chem-LUT / Chem-NEX / OLEIC ACID / Chem-P5S / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITIC ACID / PHYLLOQUINONE / PHOSPHATIDYLETHANOLAMINE / Chem-QTB / (3R)-beta,beta-caroten-3-ol / IRON/SULFUR CLUSTER / SPHINGOSINE / Chem-SQD / Chem-XAT / PSI subunit V / Photosystem I subunit O / Photosystem I reaction center subunit chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Glutathione reductase / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit VI-chloroplastic-like / Photosystem I reaction center subunit III / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI-G / PSI-K / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit VIII / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IX / Photosystem I P700 chlorophyll a apoprotein A1
Similarity search - Component
Biological speciesChlorella ohadii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsCaspy, I. / Nelson, N. / Nechushtai, R. / Neumann, E. / Shkolnisky, Y.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
German-Israeli Foundation for Research and DevelopmentG-1483-207/2018 Israel
CitationJournal: Nat Plants / Year: 2021
Title: Cryo-EM photosystem I structure reveals adaptation mechanisms to extreme high light in Chlorella ohadii.
Authors: Ido Caspy / Ehud Neumann / Maria Fadeeva / Varda Liveanu / Anton Savitsky / Anna Frank / Yael Levi Kalisman / Yoel Shkolnisky / Omer Murik / Haim Treves / Volker Hartmann / Marc M Nowaczyk / ...Authors: Ido Caspy / Ehud Neumann / Maria Fadeeva / Varda Liveanu / Anton Savitsky / Anna Frank / Yael Levi Kalisman / Yoel Shkolnisky / Omer Murik / Haim Treves / Volker Hartmann / Marc M Nowaczyk / Wolfgang Schuhmann / Matthias Rögner / Itamar Willner / Aaron Kaplan / Gadi Schuster / Nathan Nelson / Wolfgang Lubitz / Rachel Nechushtai /
Abstract: Photosynthesis in deserts is challenging since it requires fast adaptation to rapid night-to-day changes, that is, from dawn's low light (LL) to extreme high light (HL) intensities during the daytime. ...Photosynthesis in deserts is challenging since it requires fast adaptation to rapid night-to-day changes, that is, from dawn's low light (LL) to extreme high light (HL) intensities during the daytime. To understand these adaptation mechanisms, we purified photosystem I (PSI) from Chlorella ohadii, a green alga that was isolated from a desert soil crust, and identified the essential functional and structural changes that enable the photosystem to perform photosynthesis under extreme high light conditions. The cryo-electron microscopy structures of PSI from cells grown under low light (PSI) and high light (PSI), obtained at 2.70 and 2.71 Å, respectively, show that part of light-harvesting antenna complex I (LHCI) and the core complex subunit (PsaO) are eliminated from PSI to minimize the photodamage. An additional change is in the pigment composition and their number in LHCI; about 50% of chlorophyll b is replaced by chlorophyll a. This leads to higher electron transfer rates in PSI and might enable C. ohadii PSI to act as a natural photosynthesiser in photobiocatalytic systems. PSI or PSI were attached to an electrode and their induced photocurrent was determined. To obtain photocurrents comparable with PSI, 25 times the amount of PSI was required, demonstrating the high efficiency of PSI. Hence, we suggest that C. ohadii PSI is an ideal candidate for the design of desert artificial photobiocatalytic systems.
History
DepositionAug 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit chloroplastic
E: Photosystem I reaction center subunit IV
F: PSI-F
G: Photosystem I reaction center subunit chloroplastic
H: Photosystem I reaction center subunit VI-chloroplastic-like
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit chloroplastic
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
I: Photosystem I reaction center subunit VIII
O: Photosystem I subunit O
1: Chlorophyll a-b binding protein, chloroplastic
a: Chlorophyll a-b binding protein, chloroplastic
3: Glutathione reductase
4: Lhca4
5: Chlorophyll a-b binding protein, chloroplastic
6: Chlorophyll a-b binding protein, chloroplastic
7: Lhca7
8: Chlorophyll a-b binding protein, chloroplastic
2: Chlorophyll a-b binding protein, chloroplastic
9: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)827,344427
Polymers511,63224
Non-polymers315,712403
Water1,78399
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  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I ... , 13 types, 13 molecules ABCDEGHJKLMIO

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PSI-A / PsaA


Mass: 82125.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SY74, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 81544.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SUA3, photosystem I
#3: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8723.009 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SKM2, photosystem I
#4: Protein Photosystem I reaction center subunit chloroplastic /


Mass: 15958.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TKF8
#5: Protein Photosystem I reaction center subunit IV /


Mass: 7194.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6U4S6
#7: Protein Photosystem I reaction center subunit chloroplastic /


Mass: 10326.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TZI8
#8: Protein Photosystem I reaction center subunit VI-chloroplastic-like /


Mass: 10319.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TPU7
#9: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J


Mass: 4475.292 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SUD1
#10: Protein Photosystem I reaction center subunit chloroplastic /


Mass: 8725.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6U0J1
#11: Protein Photosystem I reaction center subunit XI /


Mass: 16501.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TC44
#12: Protein/peptide Photosystem I reaction center subunit XII / / PSI-M


Mass: 3376.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SU98
#13: Protein/peptide Photosystem I reaction center subunit VIII / / PSI-I


Mass: 3856.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SIP9
#14: Protein Photosystem I subunit O /


Mass: 9547.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6THB2

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Protein , 4 types, 4 molecules F347

#6: Protein PSI-F


Mass: 18069.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TPV8
#16: Protein Glutathione reductase /


Mass: 26163.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TMT4
#17: Protein Lhca4


Mass: 23010.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant)
#20: Protein Lhca7


Mass: 24016.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant)

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Chlorophyll a-b binding protein, ... , 6 types, 7 molecules 1a56829

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


Mass: 19933.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TT36
#18: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 25371.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6U4K1
#19: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 25316.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TPR7
#21: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23612.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TZ50
#22: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23618.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TMX4
#23: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 19911.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TMI2

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Sugars , 2 types, 8 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#36: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 29 types, 494 molecules

#24: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#25: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 208 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#26: Chemical...
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#27: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#28: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#29: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C40H56
#30: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#31: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#32: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C41H78O12S
#33: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#34: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 704.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H77O8P
#37: Chemical
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#38: Chemical ChemComp-LPX / (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate


Mass: 453.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44NO7P
#39: Chemical 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 / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL / 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O4
#40: Chemical ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin / Β-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O
#41: Chemical
ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H37NO2
#42: Chemical ChemComp-ECH / beta,beta-caroten-4-one / echinenone / Echinenone


Mass: 550.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54O
#43: Chemical...
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN / Lutein


Mass: 568.871 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C40H56O2
#44: Chemical ChemComp-AXT / ASTAXANTHIN / 3,3'-DIHYDROXY-BETA,BETA-CAROTENE-4,4'-DIONE / Astaxanthin


Mass: 596.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H52O4
#45: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#46: Chemical ChemComp-QTB / (3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one


Mass: 260.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H28O
#47: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C16H32O2
#48: Chemical
ChemComp-DGA / DIACYL GLYCEROL / Diglyceride


Mass: 625.018 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H76O5
#49: Chemical ChemComp-13X / benzene-1,3,5-triol / Phloroglucinol / Phloroglucinol


Mass: 126.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O3
#50: Chemical
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 / VIOLAXANTHIN / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O4
#51: Chemical ChemComp-4RF / Tripalmitoylglycerol / propane-1,2,3-triyl trihexadecanoate / Tripalmitin


Mass: 807.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C51H98O6
#52: Chemical ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine / Phosphatidylserine


Mass: 792.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO10P
#53: Chemical ChemComp-LAP / [2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETHYL]-TRIMETHYLAMMONIUM / L-ALFA-LYSOPHOSPHATIDYLCHOLINE, LAUROYL


Mass: 440.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H43NO7P
#54: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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 / Type: COMPLEX / Entity ID: #1-#23 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Chlorella ohadii (plant)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 1.4 sec. / Electron dose: 49.05 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 4926

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Processing

Software
NameVersionClassification
phenix.real_space_refinedev_3951refinement
PHENIXdev_3951refinement
EM software
IDNameVersionCategoryDetails
4CTFFIND4.1.13CTF correction
7PHENIXmodel fittingphenix.dock_in_map
9RELION3.0.7initial Euler assignment
10RELION3.0.7final Euler assignment
11RELION3.0.7classification
12RELION3.0.73D reconstruction
13PHENIXmodel refinementphenix.real_space_refine
CTF correctionType: NONE
Particle selectionNum. of particles selected: 553691
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185138 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 74.16 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6IJO

6ijo

RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 30.18 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005559414
ELECTRON MICROSCOPYf_angle_d1.842983542
ELECTRON MICROSCOPYf_chiral_restr0.10196993
ELECTRON MICROSCOPYf_plane_restr0.007516429
ELECTRON MICROSCOPYf_dihedral_angle_d26.730616746

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