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- PDB-7pi5: Unstacked stretched Dunaliella PSII -

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Basic information

Entry
Database: PDB / ID: 7pi5
TitleUnstacked stretched Dunaliella PSII
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 13
  • CP26
  • CP29
  • Chlorophyll a-b binding protein, chloroplastic
  • Hypothetical protein
  • LHCII M1
  • LHCII M3
  • PSII 6.1 kDa protein
  • PsbO
  • PsbP
  • PsbU
KeywordsPHOTOSYNTHESIS / green algae / photosystem II / thylakoid / oxygen evolving complex / cryo-EM / stacking
Function / homology
Function and homology information


plastoglobule / photosynthesis, light harvesting / oxygen evolving activity / photosynthesis, light harvesting in photosystem I / photosystem II stabilization / photosystem II reaction center / photosystem II / chloroplast envelope / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain ...plastoglobule / photosynthesis, light harvesting / oxygen evolving activity / photosynthesis, light harvesting in photosystem I / photosystem II stabilization / photosystem II reaction center / photosystem II / chloroplast envelope / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / response to herbicide / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem II / chloroplast thylakoid membrane / phosphate ion binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / response to light stimulus / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM ...Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / BICARBONATE ION / Chem-C7Z / CHLOROPHYLL B / CHLOROPHYLL A / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / BICARBONATE ION / Chem-C7Z / CHLOROPHYLL B / CHLOROPHYLL A / DIACYL GLYCEROL / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LMK / Chem-LPX / Chem-LUT / Chem-NEX / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / (3R)-beta,beta-caroten-3-ol / SPHINGOSINE / Chem-SQD / Chem-XAT / Photosystem II D2 protein / Photosystem II reaction center protein J / Photosystem II reaction center protein H / Cytochrome b559 subunit beta / Chlorophyll a-b binding protein, chloroplastic / PSII 6.1 kDa protein / Photosystem II PsbX / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center protein K / Photosystem II reaction center protein I / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Z / Photosystem II reaction center protein M / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II protein D1 / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein L
Similarity search - Component
Biological speciesDunaliella salina (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsCaspy, I. / Fadeeva, M. / Mazor, Y. / Nelson, N.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
Israel Science Foundation199/21 Israel
CitationJournal: Elife / Year: 2023
Title: Structure of photosystem II reveals conformational flexibility of stacked and unstacked supercomplexes.
Authors: Ido Caspy / Maria Fadeeva / Yuval Mazor / Nathan Nelson /
Abstract: Photosystem II (PSII) generates an oxidant whose redox potential is high enough to enable water oxidation , a substrate so abundant that it assures a practically unlimited electron source for life on ...Photosystem II (PSII) generates an oxidant whose redox potential is high enough to enable water oxidation , a substrate so abundant that it assures a practically unlimited electron source for life on earth . Our knowledge on the mechanism of water photooxidation was greatly advanced by high-resolution structures of prokaryotic PSII . Here, we show high-resolution cryogenic electron microscopy (cryo-EM) structures of eukaryotic PSII from the green alga at two distinct conformations. The conformers are also present in stacked PSII, exhibiting flexibility that may be relevant to the grana formation in chloroplasts of the green lineage. CP29, one of PSII associated light-harvesting antennae, plays a major role in distinguishing the two conformations of the supercomplex. We also show that the stacked PSII dimer, a form suggested to support the organisation of thylakoid membranes , can appear in many different orientations providing a flexible stacking mechanism for the arrangement of grana stacks in thylakoids. Our findings provide a structural basis for the heterogenous nature of the eukaryotic PSII on multiple levels.
History
DepositionAug 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
V: Photosystem II reaction center protein Ycf12
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: PsbO
P: PsbP
T: Photosystem II reaction center protein T
W: PSII 6.1 kDa protein
X: Hypothetical protein
Z: Photosystem II reaction center protein Z
N: LHCII M3
G: Chlorophyll a-b binding protein, chloroplastic
R: CP29
S: CP26
Y: LHCII M1
U: PsbU
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
v: Photosystem II reaction center protein Ycf12
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: PsbO
p: PsbP
t: Photosystem II reaction center protein T
w: PSII 6.1 kDa protein
x: Hypothetical protein
z: Photosystem II reaction center protein Z
n: LHCII M3
g: Chlorophyll a-b binding protein, chloroplastic
r: CP29
s: CP26
y: LHCII M1
u: PsbU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,081,345393
Polymers814,57750
Non-polymers266,769343
Water12,935718
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem II ... , 13 types, 26 molecules AaBbVvCcDdHhIiJjKkLlMmTtZz

#1: Protein Photosystem II protein D1 / PSII D1 protein / Photosystem II Q(B) protein


Mass: 37291.488 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FY08, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 53289.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FY05
#3: Protein/peptide Photosystem II reaction center protein Ycf12


Mass: 3217.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FY13
#4: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 49128.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXY3
#5: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 38965.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: A0A1C8XRK9, photosystem II
#8: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7124.381 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: A0A1C8XRP3
#9: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 3929.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXX5
#10: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 3737.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: A0A1C8XRM8
#11: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4159.991 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXX2
#12: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4417.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FY19
#13: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3437.093 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXZ3
#16: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3478.194 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FY04
#19: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6430.616 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FXZ2

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#6: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 8743.847 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: D0FY01
#7: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 3549.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: A0A1C8XRP4

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Protein , 7 types, 14 molecules OoPpNnGgRrSsYy

#14: Protein PsbO


Mass: 25874.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#15: Protein PsbP


Mass: 20425.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#20: Protein LHCII M3


Mass: 24075.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#21: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23719.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: A1XKU7
#22: Protein CP29


Mass: 21748.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)
#23: Protein CP26


Mass: 26233.607 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: A0A7S3VRZ8
#24: Protein LHCII M1


Mass: 23537.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: A0A6S8N9J6

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Protein/peptide , 3 types, 6 molecules WwXxUu

#17: Protein/peptide PSII 6.1 kDa protein


Mass: 4698.315 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: A0A7S3QU88
#18: Protein/peptide Hypothetical protein


Mass: 2854.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant) / References: UniProt: A0A7S3VKF3
#25: Protein/peptide PsbU


Mass: 3219.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dunaliella salina (plant)

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Sugars , 1 types, 8 molecules

#38: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 26 types, 1053 molecules

#26: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#27: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#28: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#29: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 160 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#30: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#31: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C40H56
#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.: 6 / Source method: obtained synthetically / Formula: C41H78O12S
#33: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C45H86O10
#34: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#35: Chemical ChemComp-C7Z / (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O2
#36: Chemical
ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H76O5
#37: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#39: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#40: Chemical ChemComp-LMK / trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium


Mass: 773.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H94NO7
#41: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#42: Chemical ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#43: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#44: Chemical ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O
#45: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#46: 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


Mass: 568.871 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56O2
#47: 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


Mass: 600.870 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56O4
#48: 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.: 10 / Source method: obtained synthetically / Formula: C40H56O4
#49: Chemical ChemComp-LPX / (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate


Mass: 453.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H44NO7P
#50: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H77O8P
#51: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37NO2
#52: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / 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: Dunaliella salina Photosystem II complex / Type: COMPLEX / Entity ID: #1-#25 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Dunaliella salina (plant)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELD
Image recordingElectron dose: 51.81 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 13586

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
13RELION3.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 401467
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23014 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 6KAC

6kac


Accession code: 6KAC / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00578932
ELECTRON MICROSCOPYf_angle_d1.578109438
ELECTRON MICROSCOPYf_dihedral_angle_d22.41718735
ELECTRON MICROSCOPYf_chiral_restr0.08810418
ELECTRON MICROSCOPYf_plane_restr0.00714992

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