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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 / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / 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 reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / 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 cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Chlorophyll A-B binding protein, plant and chromista / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / 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: Nature Communications / Year: 2025
Title: Cryo-EM structure of photosystem II supercomplex from Chlorella ohadii, a green microalga with extreme phototolerance
Authors: Arshad, R. / Skalidis, I. / Kopecny, D. / Brabencova, S. / Opatikova, M. / Ilik, P. / Pospisil, P. / Hamdi, F. / Zeljkovic, S.C. / Kopecna, M. / Roudnicky, P. / Lazar, D. / Elias, E. / ...Authors: Arshad, R. / Skalidis, I. / Kopecny, D. / Brabencova, S. / Opatikova, M. / Ilik, P. / Pospisil, P. / Hamdi, F. / Zeljkovic, S.C. / Kopecna, M. / Roudnicky, P. / Lazar, D. / Elias, E. / Croce, R. / Kastritis, P. / Kouril, R.
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

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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
#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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