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- PDB-9l5v: cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332 -

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Basic information

Entry
Database: PDB / ID: 9l5v
Titlecryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 14
  • (Psb-gama_linker) x 2
  • ACPII-1
  • ACPII-2
  • ACPII-3
  • ACPII-4
  • ACPII-5
  • ACPII-6
KeywordsPHOTOSYNTHESIS / photosynthesis complex
Function / homology
Function and homology information


photosystem II / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / protein stabilization
Similarity search - Function
Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein
Similarity search - Domain/homology
BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / Chem-IHT / Chem-II0 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE ...BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / Chem-IHT / Chem-II0 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / : / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / : / Photosystem II reaction center protein H
Similarity search - Component
Biological speciesRhodomonas sp. NIES-2332 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsYonehara, N. / Akita, F. / Shen, J.R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H04916 Japan
CitationJournal: Front Plant Sci / Year: 2025
Title: Structural analysis of PSI-ACPI and PSII-ACPII supercomplexes from a cryptophyte alga sp. NIES-2332.
Authors: Wenyue Zhang / Nozomi Yonehara / Mizuki Ishii / Haowei Jiang / Romain La Rocca / Pi-Cheng Tsai / Hongjie Li / Koji Kato / Fusamichi Akita / Jian-Ren Shen
Abstract: Light energy is converted to chemical energy by two photosystems (PSI and PSII) in complex with their light-harvesting complex proteins (LHCI and LHCII) in photosynthesis. is a member of cryptophyte ...Light energy is converted to chemical energy by two photosystems (PSI and PSII) in complex with their light-harvesting complex proteins (LHCI and LHCII) in photosynthesis. is a member of cryptophyte alga whose LHCs contain unique chlorophyll proteins (ACPs) and phycobiliproteins. We purified PSI-ACPI and PSII-ACPII supercomplexes from a cryptophyte sp. NIES-2332 and analyzed their structures at high resolutions of 2.08 Å and 2.17 Å, respectively, using cryo-electron microscopy. These structures are largely similar to those reported previously from two other species of cryptophytes, but exhibited some differences in both the pigment locations and subunit structures. A part of the antenna subunits of both photosystems is shifted compared with the previously reported structures from other species of cryptophytes, suggesting some differences in the energy transfer rates from the antenna to the PSI and PSII cores. Newly identified lipids are found to occupy the interfaces between the antennae and cores, which may be important for assembly and stabilization of the supercomplexes. Water molecules surrounding three iron-sulfur clusters of the PSI core are found in our high-resolution structure, some of which are conserved from cyanobacteria to higher plants but some are different. In addition, our structure of PSII-ACPII lacks the subunits of oxygen-evolving complex as well as the MnCaO cluster, suggesting that the cells are in the S-growth phase, yet the PSI-ACPI structure showed the binding of PsaQ, suggesting that it is in an L-phase. These results suggest that the S-phase and L-phase can co-exist in the cryptophytic cells. The high-resolution structures of both PSI-ACPIs and PSII-ACPIIs solved in this study provide a more solid structural basis for elucidating the energy transfer and quenching mechanisms in this group of the organisms.
History
DepositionDec 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
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 protein M
T: Photosystem II reaction center protein T
W: Photosystem II protein W
X: Photosystem II reaction center X protein
Y: Photosystem II reaction center protein Psb30
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
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II protein M
t: Photosystem II reaction center protein T
w: Photosystem II protein W
x: Photosystem II reaction center X protein
y: Photosystem II reaction center protein Psb30
z: Photosystem II reaction center protein Z
1: ACPII-1
N: ACPII-1
2: ACPII-2
3: ACPII-3
4: ACPII-4
5: ACPII-5
6: ACPII-6
G: Psb-gama_linker
O: ACPII-2
P: ACPII-3
Q: ACPII-4
R: ACPII-5
S: ACPII-6
g: Psb-gama_linker
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,145,723409
Polymers870,13346
Non-polymers275,591363
Water12,178676
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein Photosystem II protein D1


Mass: 41541.246 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#2: Protein Photosystem II CP47 reaction center protein


Mass: 56199.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#3: Protein Photosystem II CP43 reaction center protein


Mass: 53468.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#4: Protein Photosystem II D2 protein


Mass: 39160.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#7: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7429.764 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote) / References: UniProt: A6MW35
#8: Protein/peptide Photosystem II reaction center protein I


Mass: 4390.065 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#9: Protein/peptide Photosystem II reaction center protein K


Mass: 5025.104 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#10: Protein/peptide Photosystem II reaction center protein L


Mass: 4363.087 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#11: Protein Photosystem II protein M


Mass: 11851.810 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#12: Protein/peptide Photosystem II reaction center protein T


Mass: 3708.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#13: Protein Photosystem II protein W


Mass: 12592.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#14: Protein/peptide Photosystem II reaction center X protein


Mass: 4192.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#15: Protein/peptide Photosystem II reaction center protein Psb30


Mass: 3662.478 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#16: Protein Photosystem II reaction center protein Z


Mass: 6656.092 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)

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

#5: Protein Cytochrome b559 subunit alpha


Mass: 9503.720 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#6: Protein/peptide Cytochrome b559 subunit beta


Mass: 4860.847 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)

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Protein , 8 types, 14 molecules 1N2O3P4Q5R6SGg

#17: Protein ACPII-1


Mass: 25355.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#18: Protein ACPII-2


Mass: 23785.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#19: Protein ACPII-3


Mass: 19900.920 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#20: Protein ACPII-4


Mass: 21802.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#21: Protein ACPII-5


Mass: 24844.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#22: Protein ACPII-6


Mass: 18970.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#23: Protein Psb-gama_linker


Mass: 31784.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)
#24: Protein Psb-gama_linker


Mass: 31815.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. NIES-2332 (eukaryote)

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Sugars , 1 types, 4 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 16 types, 1035 molecules

#25: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#26: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 194 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical...
ChemComp-WVN / 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene / ALPHA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#29: 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 / Feature type: SUBJECT OF INVESTIGATION
#30: 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.: 4 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#32: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#33: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#36: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#37: 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
#38: Chemical...
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C35H28MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#39: Chemical...
ChemComp-II0 / (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol / Alloxanthin


Mass: 564.840 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: C40H52O2 / Feature type: SUBJECT OF INVESTIGATION
#40: Chemical
ChemComp-IHT / (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol / Allobetaxanthin


Mass: 550.856 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H54O / Feature type: SUBJECT OF INVESTIGATION
#41: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / 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: cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332
Type: COMPLEX / Entity ID: #1-#16, #18-#22 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Rhodomonas sp. NIES-2332 (eukaryote)
Buffer solutionpH: 6.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28657 / Symmetry type: POINT
RefinementHighest resolution: 2.17 Å

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