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- PDB-7oui: Structure of C2S2M2-type Photosystem supercomplex from Arabidopsi... -

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Entry
Database: PDB / ID: 7oui
TitleStructure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana (digitonin-extracted)
Components
  • (Chlorophyll a-b binding protein ...Light-harvesting complexes of green plants) x 3
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 12
  • Chlorophyll a-b binding protein, chloroplastic
  • Lhcb1.4
  • Lhcb3.1
  • Oxygen-evolving enhancer protein 1-1, chloroplastic
  • PsbTn
  • PsbX
KeywordsPHOTOSYNTHESIS / Oxidoreductase / Complex
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem II / plastid thylakoid membrane / regulation of protein dephosphorylation / photoinhibition / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / sequestering of metal ion / chloroplast stromal thylakoid / thylakoid lumen ...photosynthesis, light harvesting in photosystem II / plastid thylakoid membrane / regulation of protein dephosphorylation / photoinhibition / photosystem II antenna complex / PSII associated light-harvesting complex II / nonphotochemical quenching / sequestering of metal ion / chloroplast stromal thylakoid / thylakoid lumen / plastoglobule / response to high light intensity / thylakoid membrane / chloroplast thylakoid / regulation of stomatal movement / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / vacuolar transport / response to abscisic acid / apoplast / photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / chloroplast envelope / : / thylakoid / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / poly(U) RNA binding / response to herbicide / photosystem II / plastid / chloroplast stroma / photosynthetic electron transport in photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / response to light stimulus / photosynthesis / chloroplast / electron transfer activity / membrane => GO:0016020 / protein stabilization / endosome / iron ion binding / protein domain specific binding / mRNA binding / heme binding / endoplasmic reticulum / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / : / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Snf7 family / Snf7 / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily ...Photosystem II 5kDa protein, chloroplastic / : / Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Snf7 family / Snf7 / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / 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 CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / 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 / 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 / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-XAT / (thale cress) hypothetical protein / 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 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 / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center W protein, chloroplastic / Photosystem II 5 kDa protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein 3, chloroplastic / Chlorophyll a-b binding protein CP26, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsGraca, A.T. / Hall, M. / Persson, K. / Schroder, W.P.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-05009 Sweden
Other privateCarl Trygger Sweden
Citation
Journal: Sci Rep / Year: 2021
Title: High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction.
Authors: André T Graça / Michael Hall / Karina Persson / Wolfgang P Schröder /
Abstract: In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the ...In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated MnCaO-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation.
History
DepositionJun 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
1: Lhcb1.4
2: Lhcb3.1
3: Lhcb1.4
4: 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 (PsbF)
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Oxygen-evolving enhancer protein 1-1, chloroplastic
T: Photosystem II reaction center protein T
W: Photosystem II reaction center W protein, chloroplastic
X: PsbX
Z: Photosystem II reaction center protein Z
S: Chlorophyll a-b binding protein CP26, chloroplastic
G: Chlorophyll a-b binding protein 1, chloroplastic
N: Chlorophyll a-b binding protein 1, chloroplastic
Y: Chlorophyll a-b binding protein 1, chloroplastic
R: Chlorophyll a-b binding protein CP29.1, chloroplastic
U: PsbTn
5: Lhcb1.4
6: Lhcb3.1
7: Lhcb1.4
8: 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 (PsbF)
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Oxygen-evolving enhancer protein 1-1, chloroplastic
t: Photosystem II reaction center protein T
w: Photosystem II reaction center W protein, chloroplastic
x: PsbX
z: Photosystem II reaction center protein Z
s: Chlorophyll a-b binding protein CP26, chloroplastic
g: Chlorophyll a-b binding protein 1, chloroplastic
n: Chlorophyll a-b binding protein 1, chloroplastic
y: Chlorophyll a-b binding protein 1, chloroplastic
r: Chlorophyll a-b binding protein CP29.1, chloroplastic
u: PsbTn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,321,043426
Polymers1,012,27452
Non-polymers308,770374
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 10 molecules 13572648Oo

#1: Protein
Lhcb1.4


Mass: 28193.934 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q39142
#2: Protein Lhcb3.1


Mass: 26452.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q9S7M0
#3: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23198.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q9LMQ2
#15: 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: 26594.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P23321

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Photosystem II ... , 12 types, 24 molecules AaBbCcDdHhIiKkLlMmTtWwZz

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


Mass: 38830.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P83755, photosystem II
#5: 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) / Variant: Wild type / References: UniProt: P56777
#6: Protein Photosystem II CP43 reaction center protein / / PSII 43 kDa protein / Protein CP-43


Mass: 50086.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P56778
#7: Protein Photosystem II D2 protein / / PSII D2 protein / Photosystem Q(A) protein


Mass: 39444.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P56761, photosystem II
#10: Protein Photosystem II reaction center protein H / / PSII-H / Photosystem II 10 kDa phosphoprotein


Mass: 7575.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P56780
#11: 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) / Variant: Wild type / References: UniProt: P62100
#12: Protein/peptide Photosystem II reaction center protein K / / PSII-K


Mass: 4239.112 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P56782
#13: 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) / Variant: Wild type / References: UniProt: P60129
#14: 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) / Variant: Wild type / References: UniProt: P62109
#16: 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) / Variant: Wild type / References: UniProt: P61839
#17: Protein Photosystem II reaction center W protein, chloroplastic / / PSII 6.1 kDa protein


Mass: 6036.749 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q39194
#19: 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) / Variant: Wild type / References: UniProt: P56790

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

#8: 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) / Variant: Wild type / References: UniProt: P56779
#9: Protein/peptide Cytochrome b559 subunit beta (PsbF) /


Mass: 4428.228 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P62095

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Protein/peptide , 2 types, 4 molecules XxUu

#18: Protein/peptide PsbX


Mass: 4186.916 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: A0A7G2E9B1
#23: Protein/peptide PsbTn


Mass: 3178.810 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q39195

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Chlorophyll a-b binding protein ... , 3 types, 10 molecules SsGNYgnyRr

#20: Protein Chlorophyll a-b binding protein CP26, chloroplastic / LHCB5 / LHCIIc / Light-harvesting complex II protein 5


Mass: 25232.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q9XF89
#21: Protein
Chlorophyll a-b binding protein 1, chloroplastic / Chlorophyll a-b protein 140 / CAB-140 / LHCII type I CAB-1


Mass: 24885.072 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: P04778
#22: Protein Chlorophyll a-b binding protein CP29.1, chloroplastic / LHCB4.1 / LHCII protein 4.1


Mass: 27302.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Variant: Wild type / References: UniProt: Q07473

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Sugars , 1 types, 8 molecules

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


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

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Non-polymers , 18 types, 505 molecules

#24: Chemical...
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#25: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 162 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#26: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#27: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#28: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-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
#30: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C45H86O10
#31: 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 / Plastoquinone


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#32: Chemical...
ChemComp-AJP / Digitonin / Digitonin


Mass: 1229.312 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C56H92O29 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#33: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#34: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#36: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#37: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#38: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#39: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN / Lutein


Mass: 568.871 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56O2
#40: 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
#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 / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O4
#42: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 - Light Harvesting Complex II supercomplex (PSII-LHCII, C2S2M2-type)COMPLEX#1-#230NATURAL
2CP24-LHCII (M-trimer)COMPLEX#1-#31NATURAL
3LHCII S-trimerCOMPLEX#21-#231NATURAL
4CP29COMPLEX#221NATURAL
5CP26COMPLEX#201NATURAL
6Photosystem II core complex (dimer)COMPLEX#4-#191NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.4 MDaYES
21NO
13
31NO
41NO
Source (natural)

Cellular location: Thylakoid Membrane / Ncbi tax-ID: 3702 / Organ: Leaf / Organelle: Chloroplast / Organism: Arabidopsis thaliana (thale cress) / Strain: Wildtype

IDEntity assembly-ID
21
32
43
54
65
76
Buffer solutionpH: 7.5 / Details: 10mM HEPES-KOH pH7.5 + 0.01% (w/v) digitonin
Buffer componentName: HEPES-KOH
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Indicated sample concentration based on Chlorophyll measurement.
Specimen supportDetails: 50 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Blot force -5 Wait time 1s Blotting time 5s

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.49 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12227

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2EPU2.7.0image acquisition
4cryoSPARC2.15CTF correction
9cryoSPARC2.15initial Euler assignment
10cryoSPARC2.15final Euler assignment
12cryoSPARC2.153D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100712 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 48.35 Å2

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