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- PDB-8xkl: Structure of ACPII-CCPII from cryptophyte algae -

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Basic information

Entry
Database: PDB / ID: 8xkl
TitleStructure of ACPII-CCPII from cryptophyte algae
Components
  • ACPII-1
  • ACPII-2
  • ACPII-3
  • ACPII-4
  • ACPII-5
  • ACPII-6
  • CCPII-S
  • Photosystem II reaction center protein G
KeywordsSTRUCTURAL PROTEIN / Photosystem II / PHOTOSYNTHESIS
Function / homologyChem-8CT / CHLOROPHYLL A / Chem-IHT / Chem-II0 / Chem-II3 / Chlorophyll c2 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-SQD
Function and homology information
Biological speciesChroomonas placoidea (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsLi, X.Y. / Mao, Z.Y. / Shen, J.R. / Han, G.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesYSBR-004 China
CitationJournal: Nat Commun / Year: 2024
Title: Structure and distinct supramolecular organization of a PSII-ACPII dimer from a cryptophyte alga Chroomonas placoidea.
Authors: Zhiyuan Mao / Xingyue Li / Zhenhua Li / Liangliang Shen / Xiaoyi Li / Yanyan Yang / Wenda Wang / Tingyun Kuang / Jian-Ren Shen / Guangye Han /
Abstract: Cryptophyte algae are an evolutionarily distinct and ecologically important group of photosynthetic unicellular eukaryotes. Photosystem II (PSII) of cryptophyte algae associates with alloxanthin ...Cryptophyte algae are an evolutionarily distinct and ecologically important group of photosynthetic unicellular eukaryotes. Photosystem II (PSII) of cryptophyte algae associates with alloxanthin chlorophyll a/c-binding proteins (ACPs) to act as the peripheral light-harvesting system, whose supramolecular organization is unknown. Here, we purify the PSII-ACPII supercomplex from a cryptophyte alga Chroomonas placoidea (C. placoidea), and analyze its structure at a resolution of 2.47 Å using cryo-electron microscopy. This structure reveals a dimeric organization of PSII-ACPII containing two PSII core monomers flanked by six symmetrically arranged ACPII subunits. The PSII core is conserved whereas the organization of ACPII subunits exhibits a distinct pattern, different from those observed so far in PSII of other algae and higher plants. Furthermore, we find a Chl a-binding antenna subunit, CCPII-S, which mediates interaction of ACPII with the PSII core. These results provide a structural basis for the assembly of antennas within the supercomplex and possible excitation energy transfer pathways in cryptophyte algal PSII, shedding light on the diversity of supramolecular organization of photosynthetic machinery.
History
DepositionDec 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: ACPII-4
7: ACPII-1
8: ACPII-2
9: ACPII-3
G: Photosystem II reaction center protein G
P: ACPII-6
p: ACPII-5
s: CCPII-S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,612120
Polymers180,0958
Non-polymers87,517112
Water00
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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Protein , 8 types, 8 molecules 0789GPps

#1: Protein ACPII-4


Mass: 23734.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#2: Protein ACPII-1


Mass: 25151.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#3: Protein ACPII-2


Mass: 23471.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#4: Protein ACPII-3


Mass: 24055.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#5: Protein Photosystem II reaction center protein G


Mass: 5464.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#6: Protein ACPII-6


Mass: 23923.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#7: Protein ACPII-5


Mass: 23762.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)
#8: Protein CCPII-S


Mass: 30531.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas placoidea (eukaryote)

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Non-polymers , 9 types, 112 molecules

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


Mass: 893.489 Da / Num. of mol.: 69 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C35H28MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#11: 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.: 5 / Source method: obtained synthetically / Formula: C40H54O
#12: 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.: 21 / Source method: obtained synthetically / Formula: C40H52O2
#13: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-II3 / (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-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol / Monadoxanthin


Mass: 566.856 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H54O2
#15: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#16: Chemical ChemComp-8CT / (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene


Mass: 536.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#17: 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.: 1 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION

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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

ComponentName: Structure of ACPII-CCPII from cryptophyte algae / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Source (natural)Organism: Chroomonas placoidea (eukaryote)
Buffer solutionpH: 7.5
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 610800 / Symmetry type: POINT

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