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- PDB-6yp7: PSII-LHCII C2S2 supercomplex from Pisum sativum grown in high lig... -

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Basic information

Entry
Database: PDB / ID: 6yp7
TitlePSII-LHCII C2S2 supercomplex from Pisum sativum grown in high light conditions
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Light harvesting chlorophyll a/b-binding protein ...) x 2
  • (Photosystem II ...) x 13
  • Chlorophyll a-b binding protein 8, chloroplastic
  • Oxygen-evolving enhancer protein 1, chloroplastic
  • Ultraviolet-B-repressible protein
KeywordsPHOTOSYNTHESIS / Cryo-EM / photosystem II / High Light
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I ...photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II / chloroplast thylakoid membrane / phosphate ion binding / photosynthesis, light reaction / : / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbX, type 1 subfamily ...Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbX, type 1 subfamily / 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 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 / 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. / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
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, chloroplastic / PSII 6.1 kDa protein / Photosystem II reaction center protein K / Photosystem II reaction center protein I / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II protein D1 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein J / Oxygen-evolving enhancer protein 1, chloroplastic / Chlorophyll a-b binding protein 8, chloroplastic / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / Photosystem II reaction center protein T / Ultraviolet-B-repressible protein / Photosystem II reaction center protein H / Photosystem II CP47 reaction center protein
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGrinzato, A. / Albanese, P. / Zanotti, G. / Pagliano, C.
CitationJournal: Int J Mol Sci / Year: 2020
Title: High-Light versus Low-Light: Effects on Paired Photosystem II Supercomplex Structural Rearrangement in Pea Plants.
Authors: Alessandro Grinzato / Pascal Albanese / Roberto Marotta / Paolo Swuec / Guido Saracco / Martino Bolognesi / Giuseppe Zanotti / Cristina Pagliano /
Abstract: In plant thylakoid membranes Photosystem II (PSII) associates with a variable number of antenna proteins (LHCII) to form different types of supercomplexes (PSII-LHCII), whose organization is ...In plant thylakoid membranes Photosystem II (PSII) associates with a variable number of antenna proteins (LHCII) to form different types of supercomplexes (PSII-LHCII), whose organization is dynamically adjusted in response to light cues, with the CS more abundant in high-light and the CSM in low-light. Paired PSII-LHCII supercomplexes interacting at their stromal surface from adjacent thylakoid membranes were previously suggested to mediate stacking. Here, we present the cryo-electron microscopy maps of paired CS and CSM supercomplexes isolated from pea plants grown in high-light and low-light, respectively. These maps show a different rotational offset between the two supercomplexes in the pair, responsible for modifying their reciprocal interaction and energetic connectivity. This evidence reveals a different way by which paired PSII-LHCII supercomplexes can mediate stacking at diverse irradiances. Electrostatic stromal interactions between LHCII trimers almost completely overlapping in the paired CS can be the main determinant by which PSII-LHCII supercomplexes mediate stacking in plants grown in high-light, whereas the mutual interaction of stromal N-terminal loops of two facing Lhcb4 subunits in the paired CSM can fulfil this task in plants grown in low-light. The high-light induced accumulation of the Lhcb4.3 protein in PSII-LHCII supercomplexes has been previously reported. Our cryo-electron microscopy map at 3.8 Å resolution of the CS supercomplex isolated from plants grown in high-light suggests the presence of the Lhcb4.3 protein revealing peculiar structural features of this high-light-specific antenna important for photoprotection.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.0Nov 25, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 25, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 25, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 25, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 25, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
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Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: database_2 / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

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Assembly

Deposited unit
g: Chlorophyll a-b binding protein 8, chloroplastic
n: Chlorophyll a-b binding protein 8, chloroplastic
y: Chlorophyll a-b binding protein 8, chloroplastic
G: Chlorophyll a-b binding protein 8, chloroplastic
N: Chlorophyll a-b binding protein 8, chloroplastic
Y: Chlorophyll a-b binding protein 8, 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
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Oxygen-evolving enhancer protein 1, chloroplastic
t: Photosystem II reaction center protein T
w: Photosystem II reaction center protein W
x: Ultraviolet-B-repressible protein
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
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Oxygen-evolving enhancer protein 1, chloroplastic
T: Photosystem II reaction center protein T
W: Photosystem II reaction center protein W
X: Ultraviolet-B-repressible protein
Z: Photosystem II reaction center protein Z
r: Light harvesting chlorophyll a/b-binding protein Lhcb4.3
s: Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26
S: Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26
R: Light harvesting chlorophyll a/b-binding protein Lhcb4.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,027,857369
Polymers768,18344
Non-polymers259,674325
Water00
1


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

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Components

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Protein , 2 types, 8 molecules gnyGNYoO

#1: Protein
Chlorophyll a-b binding protein 8, chloroplastic / LHCII type I CAB-8


Mass: 23573.473 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: CAB8, LHCB1 / Production host: Pisum sativum (garden pea) / References: UniProt: P27490
#14: Protein Oxygen-evolving enhancer protein 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 / OEC 33 kDa subunit


Mass: 26554.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: PSBO / Production host: Pisum sativum (garden pea) / References: UniProt: P14226

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

#2: Protein Photosystem II protein D1 / PSII D1 protein / 32 kDa thylakoid membrane protein / Photosystem II Q(B) protein


Mass: 36972.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbA, pgiI / Production host: Pisum sativum (garden pea) / References: UniProt: P06585, photosystem II
#3: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 55659.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbB / Production host: Pisum sativum (garden pea) / References: UniProt: Q9XQR6
#4: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Photosystem II 44 kDa chlorophyll apoprotein / Protein CP-43


Mass: 49275.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbC / Production host: Pisum sativum (garden pea) / References: UniProt: P06004
#5: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 38220.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbD / Production host: Pisum sativum (garden pea) / References: UniProt: P06006, photosystem II
#8: Protein Photosystem II reaction center protein H / PSII-H / Photosystem II 10 kDa phosphoprotein / Photosystem II 9 kDa phosphoprotein


Mass: 6455.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbH / Production host: Pisum sativum (garden pea) / References: UniProt: Q9XQR3
#9: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 3926.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbI / Production host: Pisum sativum (garden pea) / References: UniProt: D5MAJ9
#10: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 3598.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbJ / Production host: Pisum sativum (garden pea) / References: UniProt: P13555
#11: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4287.155 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbK / Production host: Pisum sativum (garden pea) / References: UniProt: D5MAJ8
#12: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4366.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbL / Production host: Pisum sativum (garden pea) / References: UniProt: P60147
#13: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3641.425 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbM / Production host: Pisum sativum (garden pea) / References: UniProt: P69529
#15: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3692.472 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbT / Production host: Pisum sativum (garden pea) / References: UniProt: Q8HS25
#16: Protein Photosystem II reaction center protein W / Photosystem II reaction center protein W / PSBW


Mass: 5914.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) / References: UniProt: A0A2D0TCJ2
#18: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6555.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbZ, ycf9 / Production host: Pisum sativum (garden pea) / References: UniProt: Q32902

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

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


Mass: 8624.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbE / Production host: Pisum sativum (garden pea) / References: UniProt: P13554
#7: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 3396.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: psbF / Production host: Pisum sativum (garden pea) / References: UniProt: P62096

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Light harvesting chlorophyll a/b-binding protein ... , 2 types, 4 molecules rRsS

#19: Protein Light harvesting chlorophyll a/b-binding protein Lhcb4.3


Mass: 24460.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea)
#20: Protein Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26


Mass: 23839.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) / References: UniProt: A0A2D0TCJ1*PLUS

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Protein/peptide / Sugars , 2 types, 12 molecules xX

#17: Protein/peptide Ultraviolet-B-repressible protein


Mass: 3929.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Pisum sativum (garden pea) / References: UniProt: Q8VYY1
#35: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 16 types, 315 molecules

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


Mass: 907.472 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#22: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 150 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#23: 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.: 12 / Source method: obtained synthetically / Formula: C40H56O2
#24: 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
#25: 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.: 7 / Source method: obtained synthetically / Formula: C40H56O4
#26: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#27: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


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


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#30: Chemical
ChemComp-PHO / PHEOPHYTIN A


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


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#32: 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
#33: 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
#34: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#36: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C45H86O10
#37: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Details

Has ligand of interestN
Has protein modificationN

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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: PSII-LHCII C2S2 supercomplex / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL
Source (natural)Organism: Pisum sativum (garden pea)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1140GATAN K2 BASE (4k x 4k)
2140GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27942 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01374954
ELECTRON MICROSCOPYf_angle_d1.367104082
ELECTRON MICROSCOPYf_dihedral_angle_d15.86137590
ELECTRON MICROSCOPYf_chiral_restr0.0639554
ELECTRON MICROSCOPYf_plane_restr0.00512585

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