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- PDB-9kqb: PSII-FCPII supercomplex from haptophyte Chrysotila roscoffensis -

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Basic information

Entry
Database: PDB / ID: 9kqb
TitlePSII-FCPII supercomplex from haptophyte Chrysotila roscoffensis
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Fucoxanthin chlorophyll a/c binding protein II (FCPII- ...) x 4
  • (Photosystem II ...) x 13
  • Light harvesting protein
KeywordsPHOTOSYNTHESIS / photosystem II / chlorophyll / light-harvesting complex / energy transfer / LHCII / FCPII / coccolithophore / haptophyte
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / response to herbicide / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem II / chloroplast thylakoid membrane ...thylakoid membrane / photosynthesis, light harvesting / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / response to herbicide / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem II / chloroplast thylakoid membrane / : / photosynthesis / chloroplast / electron transfer activity / oxidoreductase activity / iron ion binding / heme binding / metal ion binding / membrane
Similarity search - Function
Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II CP47 reaction centre protein / Photosystem II protein D1 ...Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II CP47 reaction centre protein / 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. / : / 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 / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE ...Chem-A86 / BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein T / Light harvesting protein / Photosystem II protein D1 / H(+)-exporting diphosphatase / Photosystem II reaction center protein L / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II D2 protein / Photosystem II CP47 reaction center protein
Similarity search - Component
Biological speciesChrysotila roscoffensis (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.22 Å
AuthorsLa Rocca, R. / Kato, K. / Tsai, P.-C. / Nakajima, Y. / Akita, F. / Shen, J.-R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structure of a photosystem II-FCPII supercomplex from a haptophyte reveals a distinct antenna organization.
Authors: Romain La Rocca / Koji Kato / Pi-Cheng Tsai / Yoshiki Nakajima / Fusamichi Akita / Jian-Ren Shen /
Abstract: Haptophytes are unicellular algae that produce 30 to 50% of biomass in oceans. Among haptophytes, a subset named coccolithophores is characterized by calcified scales. Despite the importance of ...Haptophytes are unicellular algae that produce 30 to 50% of biomass in oceans. Among haptophytes, a subset named coccolithophores is characterized by calcified scales. Despite the importance of coccolithophores in global carbon fixation and CaCO production, their energy conversion system is still poorly known. Here we report a cryo-electron microscopic structure of photosystem II (PSII)-fucoxanthin chlorophyll c-binding protein (FCPII) supercomplex from Chyrostila roscoffensis, a representative of coccolithophores. This complex has two sets of six dimeric and monomeric FCPIIs, with distinct orientations. Interfaces of both FCPII/FCPII and FCPII/core differ from previously reported. We also determine the sequence of Psb36, a subunit previously found in diatoms and red algae. The principal excitation energy transfer (EET) pathways involve mainly 5 FCPIIs, where one FCPII monomer mediates EET to CP47. Our findings provide a solid structural basis for EET and energy dissipation pathways occurring in coccolithophores.
History
DepositionNov 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Fucoxanthin chlorophyll a/c binding protein II (FCPII-1)
6: Fucoxanthin chlorophyll a/c binding protein II (FCPII-5)
7: Fucoxanthin chlorophyll a/c binding protein II (FCPII-1)
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H (psbH)
I: Photosystem II reaction center protein I (psbI)
J: Fucoxanthin chlorophyll a/c binding protein II (FCPII-5)
K: Photosystem II reaction center protein K (psbK)
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M (psbM)
N: Photosystem II reaction center protein Psb36
T: Photosystem II reaction center protein T
W: Photosystem II reaction center protein W (psbW)
X: Photosystem II reaction center protein X (psbX)
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H (psbH)
i: Photosystem II reaction center protein I (psbI)
k: Photosystem II reaction center protein K (psbK)
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M (psbM)
n: Photosystem II reaction center protein Psb36
t: Photosystem II reaction center protein T
w: Photosystem II reaction center protein W (psbW)
x: Photosystem II reaction center protein X (psbX)
2: Fucoxanthin chlorophyll a/c binding protein II (FCPII-2)
8: Fucoxanthin chlorophyll a/c binding protein II (FCPII-2)
D: Photosystem II D2 protein
d: Photosystem II D2 protein
C: Photosystem II CP43 reaction center protein
c: Photosystem II CP43 reaction center protein
9: Light harvesting protein
3: Light harvesting protein
4: Fucoxanthin chlorophyll a/c binding protein II (FCPII-4)
5: Fucoxanthin chlorophyll a/c binding protein II (FCPII-1)
g: Fucoxanthin chlorophyll a/c binding protein II (FCPII-1)
G: Fucoxanthin chlorophyll a/c binding protein II (FCPII-4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)977,752347
Polymers741,00042
Non-polymers236,752305
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Fucoxanthin chlorophyll a/c binding protein II (FCPII- ... , 4 types, 10 molecules 175g6J284G

#1: Protein
Fucoxanthin chlorophyll a/c binding protein II (FCPII-1)


Mass: 18307.840 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#2: Protein Fucoxanthin chlorophyll a/c binding protein II (FCPII-5)


Mass: 18451.154 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#16: Protein Fucoxanthin chlorophyll a/c binding protein II (FCPII-2)


Mass: 24920.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#20: Protein Fucoxanthin chlorophyll a/c binding protein II (FCPII-4)


Mass: 18438.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)

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

#3: Protein Photosystem II protein D1


Mass: 39588.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote) / References: UniProt: A0A7S4BZA9
#4: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56324.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote) / References: UniProt: Q4G3C5
#7: Protein Photosystem II reaction center protein H (psbH)


Mass: 7259.597 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#8: Protein/peptide Photosystem II reaction center protein I (psbI)


Mass: 4461.228 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#9: Protein/peptide Photosystem II reaction center protein K (psbK)


Mass: 4461.356 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#10: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4393.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote) / References: UniProt: D9MYJ9
#11: Protein Photosystem II reaction center protein M (psbM)


Mass: 13414.595 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#12: Protein/peptide Photosystem II reaction center protein Psb36


Mass: 3458.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote) / References: UniProt: A0A7S4C3N2
#13: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3776.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote) / References: UniProt: A0A3S6R2W1
#14: Protein Photosystem II reaction center protein W (psbW)


Mass: 5643.089 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#15: Protein/peptide Photosystem II reaction center protein X (psbX)


Mass: 3674.456 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote)
#17: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39143.762 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote) / References: UniProt: Q4G395, photosystem II
#18: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 48733.730 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote) / References: UniProt: A0A075DWU3

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

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


Mass: 9220.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote) / References: UniProt: Q4G380
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4858.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote) / References: UniProt: Q4G381

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Protein , 1 types, 2 molecules 93

#19: Protein Light harvesting protein


Mass: 23662.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chrysotila roscoffensis (eukaryote) / References: UniProt: A0A7S4BJL5

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Sugars , 2 types, 17 molecules

#29: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#30: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 14 types, 469 molecules

#21: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 156 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical
ChemComp-DD6 / (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical...
ChemComp-A86 / (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate / Fucoxanthin


Mass: 658.906 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C42H58O6 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical...
ChemComp-KC1 / Chlorophyll c1


Mass: 610.941 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C35H30MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#28: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#31: 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.: 5 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / 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 / Feature type: SUBJECT OF INVESTIGATION
#35: 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.: 2 / Source method: obtained synthetically / Formula: C53H80O2 / Feature type: SUBJECT OF INVESTIGATION
#36: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: Photosystem II (PSII)-fucoxanthin chlorophyll a/c binding protein II (FCPII) supercomplex from haptophyte Chrysotila roscoffensis
Type: COMPLEX
Details: PSII-FCPII supercomplex containing two sets of 6 symmetrical FCPII.
Entity ID: #5-#11, #13-#15 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
250 mMsodium chlorideNaCl1
30.05 %n-Dodecyl alpha-maltosidealpha-DDM1
SpecimenConc.: 1.53 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: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: Light was turned off during the blot.

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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: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDName
1PHENIX
2EPU
3cryoSPARC
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38582 / Algorithm: FOURIER SPACE / Num. of class averages: 12 / Symmetry type: POINT

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