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- PDB-9i4t: Photosystem II from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 9i4t
TitlePhotosystem II from Arabidopsis thaliana
Components
  • (Chlorophyll a-b binding protein ...) x 4
  • (Cytochrome b559 subunit ...) x 2
  • (Oxygen-evolving enhancer protein ...) x 3
  • (Photosystem II ...) x 14
  • Expressed protein
KeywordsPHOTOSYNTHESIS / Membrane bound / Photosystem II / Arabidopsis / Manganese cluster / oxidoreductase
Function / homology
Function and homology information


photosystem I assembly / photosystem II antenna complex / response to desiccation / response to red light / nonphotochemical quenching / chloroplast photosystem II / photoinhibition / photosynthesis, light harvesting in photosystem II / cellular response to abscisic acid stimulus / PSII associated light-harvesting complex II ...photosystem I assembly / photosystem II antenna complex / response to desiccation / response to red light / nonphotochemical quenching / chloroplast photosystem II / photoinhibition / photosynthesis, light harvesting in photosystem II / cellular response to abscisic acid stimulus / PSII associated light-harvesting complex II / cellular response to water deprivation / chloroplast stromal thylakoid / response to low light intensity stimulus / thylakoid lumen / salicylic acid binding / plastid thylakoid membrane / plastoglobule / regulation of stomatal closure / response to far red light / thylakoid membrane / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / apoplast / photosystem II oxygen evolving complex / photosystem II assembly / thylakoid / chloroplast thylakoid lumen / oxygen evolving activity / photosystem II stabilization / protein phosphatase regulator activity / 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 / photosystem II / response to herbicide / extrinsic component of membrane / chloroplast stroma / plastid / poly(U) RNA binding / photosynthetic electron transport in photosystem II / chlorophyll binding / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / positive regulation of reactive oxygen species biosynthetic process / response to light stimulus / photosynthesis / response to cold / chloroplast / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / heme binding / calcium ion binding / mitochondrion / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / 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 ...Photosystem II 5kDa protein, chloroplastic / 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 / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / 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 protein D1 / Photosystem II reaction centre protein H / 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 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
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 / Chem-LUT ...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 / Chem-LUT / Chem-NEX / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-XAT / Chlorophyll a-b binding protein 1, chloroplastic / Oxygen-evolving enhancer protein 1-1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein J / Photosystem II reaction center protein K / Photosystem II reaction center protein Z / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Photosystem II protein D1 / Chlorophyll a-b binding protein CP29.1, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Photosystem II 5 kDa protein, chloroplastic / Oxygen-evolving enhancer protein 2-1, chloroplastic / Chlorophyll a-b binding protein 2.1, chloroplastic / Expressed protein / Chlorophyll a-b binding protein CP26, chloroplastic / Oxygen-evolving enhancer protein 3-1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsForsman, J.A. / Graca, A.T. / Hussein, R. / Hall, M. / Messinger, J. / Schroder, W.P. / Aydin, A.O.
Funding support Sweden, Germany, 5items
OrganizationGrant numberCountry
Sven och Lilly Lawskis fond for naturvetenskaplig forskning Sweden
Swedish Research Council2020-03809 Sweden
Carl Trygger FoundationCTS 19.324 Sweden
Kempe FoundationJCK-2030 Sweden
German Research Foundation (DFG)TP A5 Germany
CitationJournal: To Be Published
Title: Photosystem II from Arabidopsis thaliana
Authors: Forsman, J.A. / Graca, A.T. / Hussein, R. / Hall, M. / Messinger, J. / Schroder, W.P. / Aydin, A.O.
History
DepositionJan 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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 1, chloroplastic
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 1, chloroplastic
O: Oxygen-evolving enhancer protein 1-1, chloroplastic
P: Oxygen-evolving enhancer protein 2-1, chloroplastic
Q: Oxygen-evolving enhancer protein 3-1, chloroplastic
R: Chlorophyll a-b binding protein CP29.1, chloroplastic
S: Chlorophyll a-b binding protein CP26, chloroplastic
T: Photosystem II reaction center protein T
U: Photosystem II 5 kDa protein, chloroplastic
W: Photosystem II reaction center W protein, chloroplastic
X: Expressed protein
Y: Chlorophyll a-b binding protein 2.1, 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 1, chloroplastic
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 1, chloroplastic
o: Oxygen-evolving enhancer protein 1-1, chloroplastic
p: Oxygen-evolving enhancer protein 2-1, chloroplastic
q: Oxygen-evolving enhancer protein 3-1, chloroplastic
r: Chlorophyll a-b binding protein CP29.1, chloroplastic
s: Chlorophyll a-b binding protein CP26, chloroplastic
t: Photosystem II reaction center protein T
u: Photosystem II 5 kDa protein, chloroplastic
w: Photosystem II reaction center W protein, chloroplastic
x: Expressed protein
y: Chlorophyll a-b binding protein 2.1, chloroplastic
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,288,897382
Polymers1,024,74350
Non-polymers264,154332
Water21,7261206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

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


Mass: 38961.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P83755, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56091.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56777
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 51915.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56778
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39575.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56761, photosystem II
#8: Protein Photosystem II reaction center protein H / PSII-H / Photosystem II 10 kDa phosphoprotein


Mass: 7706.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56780
#9: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 4170.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P62100
#10: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 4117.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56781
#11: Protein Photosystem II reaction center protein K / PSII-K


Mass: 6977.381 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56782
#12: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4471.075 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P60129
#13: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3783.538 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P62109
#19: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3825.642 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P61839
#20: Protein Photosystem II 5 kDa protein, chloroplastic / PSII-T / Nuclear encoded psbT / PsbTn


Mass: 11042.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q39195
#21: Protein Photosystem II reaction center W protein, chloroplastic / PSII 6.1 kDa protein


Mass: 13685.823 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q39194
#24: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6569.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56790

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

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


Mass: 9393.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P56779
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4488.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P62095

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Chlorophyll a-b binding protein ... , 4 types, 10 molecules GNgnRrSsYy

#7: Protein
Chlorophyll a-b binding protein 1, chloroplastic / Chlorophyll a-b protein 140 / CAB-140 / LHCII type I CAB-1


Mass: 28266.062 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P04778
#17: Protein Chlorophyll a-b binding protein CP29.1, chloroplastic / LHCB4.1 / LHCII protein 4.1


Mass: 31170.338 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q07473
#18: Protein Chlorophyll a-b binding protein CP26, chloroplastic / LHCB5 / LHCIIc / Light-harvesting complex II protein 5


Mass: 30187.576 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q9XF89
#23: Protein Chlorophyll a-b binding protein 2.1, chloroplastic / Photosystem II light harvesting complex gene 2.1 / Protein LIGHT-HARVESTING CHLOROPHYLL B-BINDING 2.1


Mass: 28673.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q9SHR7

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Oxygen-evolving enhancer protein ... , 3 types, 6 molecules OoPpQq

#14: Protein Oxygen-evolving enhancer protein 1-1, chloroplastic / OEE1 / 33 kDa subunit of oxygen evolving system of photosystem II / 33 kDa thylakoid membrane ...OEE1 / 33 kDa subunit of oxygen evolving system of photosystem II / 33 kDa thylakoid membrane protein / Manganese-stabilizing protein 1 / MSP-1 / OEC 33 kDa subunit


Mass: 35180.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: P23321
#15: Protein Oxygen-evolving enhancer protein 2-1, chloroplastic / OEE2 / 23 kDa subunit of oxygen evolving system of photosystem II / 23 kDa thylakoid membrane ...OEE2 / 23 kDa subunit of oxygen evolving system of photosystem II / 23 kDa thylakoid membrane protein / OEC 23 kDa subunit / OEC23


Mass: 28125.189 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q42029
#16: Protein Oxygen-evolving enhancer protein 3-1, chloroplastic / OEE3 / 16 kDa subunit of oxygen evolving system of photosystem II / OEC 16 kDa subunit


Mass: 23899.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q9XFT3

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Protein , 1 types, 2 molecules Xx

#22: Protein Expressed protein / PSBX / Photosystem II subunit X / Putative PSII-X protein / Putative uncharacterized protein ...PSBX / Photosystem II subunit X / Putative PSII-X protein / Putative uncharacterized protein At2g06520 / T12H3.7


Mass: 11826.013 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Tissue: Leaves / References: UniProt: Q9SKI3

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Sugars , 2 types, 12 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION
#36: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 17 types, 1526 molecules

#25: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 893.489 Da / Num. of mol.: 156 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#27: Chemical
ChemComp-PHO / PHEOPHYTIN A


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


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#29: 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 / Feature type: SUBJECT OF INVESTIGATION
#30: 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
#31: 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
#32: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#34: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10
#35: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5 / Feature type: SUBJECT OF INVESTIGATION
#37: 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
#38: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#39: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#40: 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
#41: 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
#42: 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
#43: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1206 / Source method: isolated from a natural source / Formula: H2O

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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

ComponentName: C2S2-type Photosystem II complex from Arabidopsis thaliana
Type: COMPLEX / Entity ID: #1-#24 / Source: NATURAL
Molecular weightValue: 1.118 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Organelle: Thylakoid membranes / Tissue: Leaves
Buffer solutionpH: 6
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-(N-morpholino)ethanesulfonic acidC6H13NO4S1
220 mMCalcium ChlorideCaCl21
35 mMMagnesium ChlorideMgCl21
40.6 MBetaineC5H11NO21
50.03 % w/vn-Dodecyl-b-D-maltosideC24H46O111
SpecimenConc.: 9.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Thylakoid membranes were solubilised using b-dodecylmaltoside. The C2S2-type Photosystem II complexes were isolated using sucrose gradients.
Specimen supportDetails: 50 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.17 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16450
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selection
2EPU3.4image acquisitionAFIS
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3054062
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72301 / Symmetry type: POINT
Atomic model buildingPDB-ID: 3JCU

3jcu


Accession code: 3JCU / Source name: PDB / Type: experimental model

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