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- PDB-9hd7: Cryo-EM structure of photosystem II C2S2M2L2 supercomplex from th... -

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Basic information

Entry
Database: PDB / ID: 9hd7
TitleCryo-EM structure of photosystem II C2S2M2L2 supercomplex from the green alga Chlorella ohadii
Components
  • (Chlorophyll a-b binding protein, ...) x 6
  • (Chloroplast oxygen-evolving enhancer protein ...) x 2
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 14
  • Chlorophyll a-b binding protein Lhcbm-I
  • Chloroplast PsbY
  • Chloroplast photosystem II 10 kDa protein
  • PSII 6.1 kDa protein
  • PWWP domain-containing protein
KeywordsMEMBRANE PROTEIN / supercomplex / photosynthesis / chlorophyll / algae
Function / homology
Function and homology information


chloroplast thylakoid / eukaryotic translation initiation factor 2 complex / photosynthesis, light harvesting / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / eukaryotic 48S preinitiation complex / transcription factor TFIIA complex ...chloroplast thylakoid / eukaryotic translation initiation factor 2 complex / photosynthesis, light harvesting / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / eukaryotic 48S preinitiation complex / transcription factor TFIIA complex / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / photosystem II / response to herbicide / extrinsic component of membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / photosynthesis / translation initiation factor activity / cell redox homeostasis / transcription initiation at RNA polymerase II promoter / ribosome binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / RNA binding / metal ion binding
Similarity search - Function
Photosystem II PsbR / Photosystem II PsbY, plant / Photosystem II 10 kDa polypeptide PsbR / PsbP, C-terminal / : / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 ...Photosystem II PsbR / Photosystem II PsbY, plant / Photosystem II 10 kDa polypeptide PsbR / PsbP, C-terminal / : / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, beta-barrel / 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 PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / 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. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / ALPHA-LINOLENIC ACID / Chem-LUT / Chem-NEX / CA-MN4-O5 CLUSTER / PALMITOLEIC ACID / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / STEARIC ACID / Chem-XAT / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Psb30 / Chloroplast photosystem II 10 kDa protein / Photosystem II reaction center protein M / Chloroplast oxygen-evolving enhancer protein 3 / Photosystem II reaction center protein I / Chloroplast PsbY / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSII 6.1 kDa protein / Chlorophyll a-b binding protein, chloroplastic / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / PWWP domain-containing protein / Photosystem II reaction center protein T / Photosystem II reaction center protein L / Photosystem II reaction center protein K / Cytochrome b559 subunit beta / Photosystem II protein D1 / Photosystem II reaction center protein H / Photosystem II reaction center protein Z / Cytochrome b559 subunit alpha / Photosystem II D2 protein / Photosystem II reaction center protein J / Photosystem II CP47 reaction center protein
Similarity search - Component
Biological speciesChlorella ohadii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsKopecny, D. / Kouril, R. / Ardhad, R. / Skalidis, I. / Kastritis, P.
Funding support Czech Republic, Germany, European Union, 6items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.01.01/00/22_008/0004624 Czech Republic
Czech Science Foundation23-07744S Czech Republic
Other governmentMZE-RO0423
German Research Foundation (DFG)391498659 (RTG 2467); SFB 1664 (TP D1) Germany
German Federal Ministry for Education and Research03Z22HN23; 03Z22HI2; 03COV04 Germany
European Regional Development FundZS/2016/04/78115European Union
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structure of photosystem II supercomplex from a green microalga with extreme phototolerance.
Authors: Rameez Arshad / Ioannis Skalidis / David Kopečný / Sylva Brabencová / Monika Opatíková / Petr Ilík / Pavel Pospíšil / Farzad Hamdi / Sanja Ćavar Zeljković / Martina Kopečná / ...Authors: Rameez Arshad / Ioannis Skalidis / David Kopečný / Sylva Brabencová / Monika Opatíková / Petr Ilík / Pavel Pospíšil / Farzad Hamdi / Sanja Ćavar Zeljković / Martina Kopečná / Pavel Roudnický / Dušan Lazár / Eduard Elias / Roberta Croce / Panagiotis L Kastritis / Roman Kouřil /
Abstract: Photosystem II (PSII) is essential for energy conversion during oxygenic photosynthesis in plants and algae. Chlorella ohadii, one of the fastest multiplying green algae, thrives under the harsh ...Photosystem II (PSII) is essential for energy conversion during oxygenic photosynthesis in plants and algae. Chlorella ohadii, one of the fastest multiplying green algae, thrives under the harsh desert sun but lacks the standard PSII photoprotective mechanisms involving LhcSR/PsbS proteins or protein phosphorylation. Here, we present the cryo-EM structure of the PSII supercomplex from C. ohadii at 2.9 Å resolution, which is used to determine whether the exceptional resistance to desert conditions has a structural basis in PSII. The structure reveals a distinct PsbO isoform and additional subunits, PsbR and PsbY, which enhance core complex stability through extensive interactions. Furthermore, the trimeric light-harvesting complexes (LHCII) are bound to the PSII core by specific light-harvesting proteins whose down-regulation in response to high-light conditions implies a reduction in the number of bound LHCII trimers. These structural modifications, together with the high accumulation of specific polyamines in the thylakoid membrane, play a key role in maintaining PSII stability and photoprotection, allowing C. ohadii to survive in extreme conditions.
History
DepositionNov 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Chlorophyll a-b binding protein Lhcbm-I
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
4: Chlorophyll a-b binding protein Lhcbm-I
5: Chlorophyll a-b binding protein, chloroplastic
6: Chlorophyll a-b binding protein, chloroplastic
7: Chloroplast photosystem II 10 kDa protein
8: Chloroplast photosystem II 10 kDa protein
11: Chlorophyll a-b binding protein Lhcbm-I
12: Chlorophyll a-b binding protein, chloroplastic
13: Chlorophyll a-b binding protein, chloroplastic
14: Chlorophyll a-b binding protein Lhcbm-I
15: Chlorophyll a-b binding protein, chloroplastic
16: Chlorophyll a-b binding protein, chloroplastic
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
G: Chlorophyll a-b binding protein Lhcbm-I
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
N: Chlorophyll a-b binding protein, chloroplastic
O: Chloroplast oxygen-evolving enhancer protein 1b (PsbO)
P: PWWP domain-containing protein
Q: Chloroplast oxygen-evolving enhancer protein 3
R: Chlorophyll a-b binding protein, chloroplastic
S: Chlorophyll a-b binding protein, chloroplastic
T: Photosystem II reaction center protein T
U: Chloroplast PsbY
V: Photosystem II reaction center protein Psb30
W: PSII 6.1 kDa protein
X: Photosystem II reaction center protein X (PsbX)
Y: Chlorophyll a-b binding protein, chloroplastic
Z: Photosystem II reaction center protein Z
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
g: Chlorophyll a-b binding protein Lhcbm-I
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
n: Chlorophyll a-b binding protein, chloroplastic
o: Chloroplast oxygen-evolving enhancer protein 1b (PsbO)
p: PWWP domain-containing protein
q: Chloroplast oxygen-evolving enhancer protein 3
r: Chlorophyll a-b binding protein, chloroplastic
s: Chlorophyll a-b binding protein, chloroplastic
t: Photosystem II reaction center protein T
u: Chloroplast PsbY
v: Photosystem II reaction center protein Psb30
w: PSII 6.1 kDa protein
x: Photosystem II reaction center protein X (PsbX)
y: Chlorophyll a-b binding protein, chloroplastic
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,098,239678
Polymers1,614,69866
Non-polymers483,541612
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 14 molecules 141114Gg78PpUuWw

#1: Protein
Chlorophyll a-b binding protein Lhcbm-I / Chlorophyll a-b binding protein Lhcbm-I


Mass: 26744.256 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: GenBank accession XHY80384 / Source: (natural) Chlorella ohadii (plant)
#4: Protein Chloroplast photosystem II 10 kDa protein


Mass: 14953.089 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A5P4NAS4
#19: Protein PWWP domain-containing protein


Mass: 94779.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt A0AAD5H4X0 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0AAD5H4X0
#24: Protein Chloroplast PsbY


Mass: 36784.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Uniprot accession A0A5P4NEE0 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A5P4NEE0
#26: Protein PSII 6.1 kDa protein


Mass: 49141.957 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt A0AAD5DZE4 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0AAD5DZE4

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Chlorophyll a-b binding protein, ... , 6 types, 16 molecules 251215Nn361316RrSsYy

#2: Protein
Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein Lhcbm-II


Mass: 26604.174 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0AAD5DLH1
#3: Protein Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein Lhcbm-IV


Mass: 27506.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt accession A0AAD5DXI2 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0AAD5DXI2
#5: Protein Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein Lhcbm-V


Mass: 26169.717 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0AAD5H446
#21: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 31706.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt A0AAD5E2W2 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0AAD5E2W2
#22: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 30853.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GenBank accession XJP35395 / Source: (natural) Chlorella ohadii (plant)
#28: Protein Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein Lhcbm-III


Mass: 27530.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt accession A0AAD5DNU0 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0AAD5DNU0

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Photosystem II ... , 14 types, 28 molecules AaBbCcDdHhIiJjKkLlMmTtVvXxZz

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


Mass: 39040.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SIR2, photosystem II
#7: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56199.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8TIK4
#8: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 52106.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GenBank accession AII02053 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A076EAP1
#9: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39534.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SYD4, photosystem II
#12: Protein Photosystem II reaction center protein H / PSII-H


Mass: 8575.999 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SIT0
#13: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 4386.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt acession A0A5P4ND48 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A5P4ND48
#14: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 4246.948 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt accession W8TIH6 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8TIH6
#15: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4681.705 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt A0A076EAP2 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: P56348
#16: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4391.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Uniprot W8SKK5 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: P56339
#17: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3751.495 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt A0A5P4NAV9 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A5P4NAV9
#23: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3605.399 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt W8SY98 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: P56327
#25: Protein/peptide Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein Ycf12


Mass: 3450.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt A0A076EAR3 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A076EAR3
#27: Protein Photosystem II reaction center protein X (PsbX)


Mass: 9831.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt A0AAD5H2N2 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0AAD5H2N2
#29: Protein Photosystem II reaction center protein Z


Mass: 6727.147 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt accession W8SKL0 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SKL0

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

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


Mass: 9449.626 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SU91
#11: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4722.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SIQ3

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Chloroplast oxygen-evolving enhancer protein ... , 2 types, 4 molecules OoQq

#18: Protein Chloroplast oxygen-evolving enhancer protein 1b (PsbO)


Mass: 31559.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GenBank accession XHY80383 / Source: (natural) Chlorella ohadii (plant)
#20: Protein Chloroplast oxygen-evolving enhancer protein 3


Mass: 21618.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: UniProt A0A5P4NB29 / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A5P4NB29

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Sugars , 1 types, 8 molecules

#46: 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 , 20 types, 604 molecules

#30: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 120 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 264 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#33: 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.: 42 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#34: 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.: 22 / Source method: obtained synthetically / Formula: C40H56O4
#35: 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 / Feature type: SUBJECT OF INVESTIGATION
#36: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H77O8P
#37: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#38: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#39: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#40: 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.: 8 / Source method: obtained synthetically / Formula: C41H78O12S
#41: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C45H86O10
#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.: 4 / Source method: obtained synthetically / Formula: C53H80O2 / Feature type: SUBJECT OF INVESTIGATION
#43: Chemical...
ChemComp-LNL / ALPHA-LINOLENIC ACID


Mass: 278.430 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C18H30O2
#44: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36O2
#45: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#47: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#48: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#49: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#50: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30O2

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Details

Has ligand of interestY
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Photosystem II supercomplex C2S2M2L2COMPLEX#1-#290NATURAL
2Photosystem II core complex (C2)COMPLEX#4, #6-#20, #23-#27, #291NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Chlorella ohadii (plant)2649997
32Chlorella ohadii (plant)2649997
Buffer solutionpH: 6.5
Buffer component
IDConc.NameBuffer-ID
125 mMMES1
21 MBetaine1
30.008 %n-Decyl-alpha-D-maltopyranoside1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: C2S2M2L2 PSII-supercomplex purified by the sucrose density gradient.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 279 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 90 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Scipion3particle selection
2Xmipp3particle selection
3EPU3.3image acquisition
5CTFFIND4.1CTF correction
8Coot0.9.8model fitting
10PHENIX1.21.2_5419model refinement
11cryoSPARC4.3.1.initial Euler assignment
12cryoSPARC4.3.1.final Euler assignment
13RELION3.1classification
14cryoSPARC4.3.1.3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225372 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeDetailsInitial refinement model-ID
17OUI

7oui

7OUIArabidopsis PSII supercomplex C2S2M21
28C29

8c29

8C29Spruce PSII supercomplex C2S22
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003118340
ELECTRON MICROSCOPYf_angle_d0.535165925
ELECTRON MICROSCOPYf_dihedral_angle_d18.35431610
ELECTRON MICROSCOPYf_chiral_restr0.06215008
ELECTRON MICROSCOPYf_plane_restr0.00618608

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