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- PDB-8bd3: Cryo-EM structure of the Photosystem II - LHCII supercomplex from... -

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Basic information

Entry
Database: PDB / ID: 8bd3
TitleCryo-EM structure of the Photosystem II - LHCII supercomplex from Chlorella ohadi
Components
  • (Chlorophyll a ...) x 2
  • (Chlorophyll a-b binding of ...) x 2
  • (Chlorophyll a-b binding protein, ...) x 2
  • (Chloroplast oxygen-evolving enhancer protein ...) x 2
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 16
  • Chloroplast PsbY
  • Chloroplast photosystem II 10 kDa protein
  • Multifunctional fusion protein
KeywordsPHOTOSYNTHESIS / Green alga / PSII / C.ohadi / membrane protein / Cryo-EM
Function / homology
Function and homology information


diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / chloroplast thylakoid / photosynthesis, light harvesting / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II ...diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / chloroplast thylakoid / 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 / response to herbicide / photosystem II / extrinsic component of membrane / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / : / photosynthesis / cell redox homeostasis / chloroplast / phospholipase C-activating G protein-coupled receptor signaling pathway / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / RNA binding / ATP binding / metal ion binding / membrane
Similarity search - Function
Photosystem II PsbR / Photosystem II PsbY, plant / Photosystem II 10 kDa polypeptide PsbR / Diacylglycerol kinase, accessory domain / Diacylglycerol kinase accessory domain / Diacylglycerol kinase accessory domain (presumed) / Serine incorporator/TMS membrane protein / Serine incorporator (Serinc) / : / Diacylglycerol kinase, catalytic domain ...Photosystem II PsbR / Photosystem II PsbY, plant / Photosystem II 10 kDa polypeptide PsbR / Diacylglycerol kinase, accessory domain / Diacylglycerol kinase accessory domain / Diacylglycerol kinase accessory domain (presumed) / Serine incorporator/TMS membrane protein / Serine incorporator (Serinc) / : / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / KH domain / 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 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. / K Homology domain, type 1 / : / 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 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / : / 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 / (3R)-beta,beta-caroten-3-ol / Chem-SQD / Chem-XAT / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Psb30 / Chlorophyll a-b binding protein, chloroplastic / Serine incorporator / Multifunctional fusion protein / 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 / Chloroplast oxygen-evolving enhancer protein 1 / Cytochrome b559 subunit beta / Photosystem II reaction center protein T / Photosystem II reaction center protein L / Photosystem II reaction center protein K / 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: 2.73 Å
AuthorsFadeeva, M. / Klaiman, D. / Caspy, I. / Nelson, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation199/21 Israel
CitationJournal: Cells / Year: 2023
Title: Structure of Photosystem II Reveals Protective Mechanisms against Environmental Stress.
Authors: Maria Fadeeva / Daniel Klaiman / Ido Caspy / Nathan Nelson /
Abstract: Green alga is known for its ability to carry out photosynthesis under harsh conditions. Using cryogenic electron microscopy (cryoEM), we obtained a high-resolution structure of PSII at 2.72 Å. This ...Green alga is known for its ability to carry out photosynthesis under harsh conditions. Using cryogenic electron microscopy (cryoEM), we obtained a high-resolution structure of PSII at 2.72 Å. This structure revealed 64 subunits, which encompassed 386 chlorophylls, 86 carotenoids, four plastoquinones, and several structural lipids. At the luminal side of PSII, a unique subunit arrangement was observed to protect the oxygen-evolving complex. This arrangement involved PsbO (OEE1), PsbP (OEE2), PsbB, and PsbU (a homolog of plant OEE3). PsbU interacted with PsbO, PsbC, and PsbP, thereby stabilizing the shield of the oxygen-evolving complex. Significant changes were also observed at the stromal electron acceptor side. PsbY, identified as a transmembrane helix, was situated alongside PsbF and PsbE, which enclosed cytochrome . Supported by the adjacent C-terminal helix of Psb10, these four transmembrane helices formed a bundle that shielded cytochrome from the surrounding solvent. Moreover, the bulk of Psb10 formed a protective cap, which safeguarded the quinone site and likely contributed to the stacking of PSII complexes. Based on our findings, we propose a protective mechanism that prevents Q (plastoquinone B) from becoming fully reduced. This mechanism offers insights into the regulation of electron transfer within PSII.
History
DepositionOct 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Chlorophyll a-b binding protein, chloroplastic
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding of LHCII
4: Chlorophyll a-b binding protein, chloroplastic
5: Chlorophyll a-b binding of LHCII
6: Chlorophyll a-b binding of LHCII
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, 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 of LHCII
O: Chloroplast oxygen-evolving enhancer protein 1
R: Chlorophyll a b binding CP29
S: Chlorophyll a b-binding CP26
T: Photosystem II reaction center protein T
V: Photosystem II reaction center protein Ycf12
W: Photosystem II reaction center W protein
X: Photosystem II reaction center protein X
Y: Multifunctional fusion protein
Z: Photosystem II reaction center protein Z
U: Chloroplast oxygen-evolving enhancer protein 3
0: Chlorophyll a-b binding of LHCII
7: Chlorophyll a-b binding protein, chloroplastic
8: Chlorophyll a-b binding of LHCII
9: Chlorophyll a-b binding protein, chloroplastic
p: Chlorophyll a-b binding of LHCII
q: 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, 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 of LHCII
o: Chloroplast oxygen-evolving enhancer protein 1
r: Chlorophyll a b binding CP29
s: Chlorophyll a b-binding CP26
t: Photosystem II reaction center protein T
v: Photosystem II reaction center protein Ycf12
w: Photosystem II reaction center W protein
x: Photosystem II reaction center protein X
y: Multifunctional fusion protein
z: Photosystem II reaction center protein Z
u: Chloroplast oxygen-evolving enhancer protein 3
Q1: Chloroplast PsbY
P1: Chloroplast photosystem II 10 kDa protein
q1: Chloroplast PsbY
p1: Chloroplast photosystem II 10 kDa protein
F1: Photosystem II oxygen evolving enhancer 2
f1: Photosystem II oxygen evolving enhancer 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,723,568738
Polymers1,180,98466
Non-polymers542,583672
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Chlorophyll a-b binding protein, ... , 2 types, 8 molecules 1724G9qg

#1: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23060.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TPU9
#2: Protein
Chlorophyll a-b binding protein, chloroplastic


Mass: 23850.742 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TDA6

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Chlorophyll a-b binding of ... , 2 types, 8 molecules 35N8pn60

#3: Protein
Chlorophyll a-b binding of LHCII


Mass: 23847.945 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant)
#4: Protein Chlorophyll a-b binding of LHCII


Mass: 23455.490 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant)

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Photosystem II ... , 16 types, 32 molecules AaBbCcDdHhIiJjKkLlMmTtVvWwXxZzF1f1

#5: Protein Photosystem II protein D1


Mass: 37230.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / Strain: 1 / References: UniProt: W8SIR2
#6: Protein Photosystem II CP47 reaction center protein


Mass: 55754.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8TIK4
#7: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 49161.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A076EAP1
#8: Protein Photosystem II D2 protein


Mass: 38459.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SYD4
#11: Protein Photosystem II reaction center protein H


Mass: 7223.423 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SIT0
#12: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 3871.545 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A5P4ND48
#13: Protein/peptide Photosystem II reaction center protein J


Mass: 3813.468 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8TIH6
#14: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4139.958 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: P56348
#15: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4259.966 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: P56339
#16: Protein Photosystem II reaction center protein M


Mass: 5621.872 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A5P4NAV9
#20: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3476.220 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: P56327
#21: Protein/peptide Photosystem II reaction center protein Ycf12


Mass: 3319.010 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A076EAR3
#22: Protein Photosystem II reaction center W protein


Mass: 6623.350 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant)
#23: Protein/peptide Photosystem II reaction center protein X


Mass: 3526.028 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant)
#25: Protein Photosystem II reaction center protein Z


Mass: 6727.147 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SKL0
#29: Protein Photosystem II oxygen evolving enhancer 2


Mass: 20416.791 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant)

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

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


Mass: 9204.327 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SU91
#10: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4262.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: P56310

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

#17: Protein Chloroplast oxygen-evolving enhancer protein 1


Mass: 25449.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A5P4NF37
#26: Protein Chloroplast oxygen-evolving enhancer protein 3


Mass: 15948.137 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A5P4NB29

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Chlorophyll a ... , 2 types, 4 molecules RrSs

#18: Protein Chlorophyll a b binding CP29


Mass: 25803.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant)
#19: Protein Chlorophyll a b-binding CP26


Mass: 27369.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant)

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Protein , 2 types, 4 molecules YyP1p1

#24: Protein Multifunctional fusion protein


Mass: 23863.996 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant)
References: UniProt: A0A2P6U5M3, diacylglycerol kinase (ATP)
#28: Protein Chloroplast photosystem II 10 kDa protein


Mass: 11657.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A5P4NAS4

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Protein/peptide , 1 types, 2 molecules Q1q1

#27: Protein/peptide Chloroplast PsbY


Mass: 3697.331 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A5P4NEE0

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Sugars , 2 types, 12 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15
#48: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 18 types, 884 molecules

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


Mass: 907.472 Da / Num. of mol.: 122 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#31: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 270 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#32: 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.: 36 / Source method: obtained synthetically / Formula: C40H56O2
#33: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#34: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 86 / Source method: obtained synthetically / Formula: C45H86O10
#35: Chemical
ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H56O
#36: 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
#37: 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
#38: 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.: 24 / Source method: obtained synthetically / Formula: C41H78O12S
#39: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


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


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


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


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


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#44: 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
#46: Chemical ChemComp-BCT / BICARBONATE ION


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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#49: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: Chlorella ohadii Photosystem II / Type: COMPLEX / Entity ID: #1-#29 / Source: NATURAL
Molecular weightValue: 1.7 MDa / Experimental value: YES
Source (natural)Organism: Chlorella ohadii (plant) / Cellular location: Thylakoid membrane / Organelle: Chloroplast
Buffer solutionpH: 6 / Details: 20 mM MES NaOH pH 6 0.1% alfaDM
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K

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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 / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 21341

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 734768
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94893 / Num. of class averages: 8 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 87.93 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007121946
ELECTRON MICROSCOPYf_angle_d1.615169171
ELECTRON MICROSCOPYf_dihedral_angle_d20.01649524
ELECTRON MICROSCOPYf_chiral_restr0.05615426
ELECTRON MICROSCOPYf_plane_restr0.00724693

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