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- PDB-7ymi: PSII-Pcb Dimer of Acaryochloris Marina -

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Basic information

Entry
Database: PDB / ID: 7ymi
TitlePSII-Pcb Dimer of Acaryochloris Marina
Components
  • (High light inducible ...) x 4
  • (Photosystem II ...) x 14
  • Cytochrome b559 subunit alpha
  • Unknown protein
KeywordsPHOTOSYNTHESIS / Photosystem II / Pcb
Function / homology
Function and homology information


photosystem / 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 II / response to herbicide / : ...photosystem / 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 II / response to herbicide / : / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / photosynthesis / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbZ, reaction centre / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Photosystem II PsbY / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosystem II PsbX, type 1 subfamily / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM ...Photosystem II PsbZ, reaction centre / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Photosystem II PsbY / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosystem II PsbX, type 1 subfamily / 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 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 reaction centre protein H superfamily / 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 / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Helix Hairpins / Roll / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-8CT / BICARBONATE ION / CHLOROPHYLL D / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / Chem-PL9 ...Chem-8CT / BICARBONATE ION / CHLOROPHYLL D / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Chem-ZEX / Photosystem II protein D1 2 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II D2 protein 1 / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Y / High light inducible protein / High light inducible protein / High light inducible protein / Photosystem II protein PsbI / Photosystem II protein PsbT / High light inducible protein / Photosystem II reaction center protein L / Cytochrome b559 subunit alpha / Photosystem II reaction center protein K / Photosystem II 10 kDa phosphoprotein PsbH / Photosystem II reaction center protein M / Photosystem II CP47 reaction center protein
Similarity search - Component
Biological speciesAcaryochloris marina MBIC11017 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsShen, L.L. / Gao, Y.Z. / Wang, W.D. / Zhang, X. / Shen, J.R. / Wang, P.Y. / Han, G.Y.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDY-SSW-SMC003 China
Chinese Academy of SciencesXDB17000000 China
National Basic Research Program of China (973 Program)2015CB150100 China
CitationJournal: Sci Adv / Year: 2024
Title: Structure of a unique PSII-Pcb tetrameric megacomplex in a chlorophyll -containing cyanobacterium.
Authors: Liangliang Shen / Yuanzhu Gao / Kailu Tang / Ruxi Qi / Lutang Fu / Jing-Hua Chen / Wenda Wang / Xiaomin Ma / Peiyao Li / Min Chen / Tingyun Kuang / Xing Zhang / Jian-Ren Shen / Peiyi Wang / Guangye Han /
Abstract: is a unique cyanobacterium using chlorophyll (Chl ) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of associates with a number of prochlorophyte Chl- ... is a unique cyanobacterium using chlorophyll (Chl ) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of associates with a number of prochlorophyte Chl-binding (Pcb) proteins to act as the light-harvesting system. We report here the cryo-electron microscopic structure of a PSII-Pcb megacomplex from at a 3.6-angstrom overall resolution and a 3.3-angstrom local resolution. The megacomplex is organized as a tetramer consisting of two PSII core dimers flanked by sixteen symmetrically related Pcb proteins, with a total molecular weight of 1.9 megadaltons. The structure reveals the detailed organization of PSII core consisting of 15 known protein subunits and an unknown subunit, the assembly of 4 Pcb antennas within each PSII monomer, and possible pathways of energy transfer within the megacomplex, providing deep insights into energy transfer and dissipation mechanisms within the PSII-Pcb megacomplex involved in far-red light utilization.
History
DepositionJul 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem II protein D1 2
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein 1
E: Cytochrome b559 subunit alpha
F: Photosystem II protein Y
H: Photosystem II 10 kDa phosphoprotein PsbH
I: Photosystem II protein PsbI
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
T: Photosystem II reaction center protein T
X: Photosystem II reaction center X protein
Y: Photosystem II reaction center protein Ycf12
Z: Photosystem II reaction center protein Z
2: High light inducible protein
G: Unknown protein
1: High light inducible protein
3: High light inducible protein
4: High light inducible protein
a: Photosystem II protein D1 2
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein 1
e: Cytochrome b559 subunit alpha
f: Photosystem II protein Y
h: Photosystem II 10 kDa phosphoprotein PsbH
i: Photosystem II protein PsbI
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
t: Photosystem II reaction center protein T
x: Photosystem II reaction center X protein
y: Photosystem II reaction center protein Ycf12
z: Photosystem II reaction center protein Z
6: High light inducible protein
g: Unknown protein
5: High light inducible protein
7: High light inducible protein
8: High light inducible protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,079,015352
Polymers825,08640
Non-polymers253,929312
Water00
1


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

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Components

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

#1: Protein Photosystem II protein D1 2 / PSII D1 protein 2 / Photosystem II Q(B) protein 2


Mass: 39695.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: A5A8K9, photosystem II
#2: Protein Photosystem II CP47 reaction center protein


Mass: 56518.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0CFM2
#3: Protein Photosystem II CP43 reaction center protein


Mass: 53978.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C1V7
#4: Protein Photosystem II D2 protein 1 / PSII D2 protein 1 / Photosystem Q(A) protein 1


Mass: 39291.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C1V6, photosystem II
#6: Protein Photosystem II protein Y


Mass: 11277.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C2V2
#7: Protein Photosystem II 10 kDa phosphoprotein PsbH


Mass: 7683.901 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0CDZ2
#8: Protein/peptide Photosystem II protein PsbI


Mass: 3948.692 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C5R5
#9: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4939.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6Z7
#10: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4254.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6T1
#11: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3614.302 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0CFM0
#12: Protein/peptide Photosystem II reaction center protein T


Mass: 5442.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C605
#13: Protein/peptide Photosystem II reaction center X protein


Mass: 4443.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0BYW9
#14: Protein/peptide Photosystem II reaction center protein Ycf12


Mass: 4015.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria)
#15: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6395.632 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C0S7

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High light inducible ... , 4 types, 8 molecules 26153748

#16: Protein High light inducible protein / Light harvesting chlorophyll d-binding protein 2 (PcbA)


Mass: 38753.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C3E5
#18: Protein High light inducible protein / Light harvesting chlorophyll d-binding protein 1 (PcbA)


Mass: 38612.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C576
#19: Protein High light inducible protein / Light harvesting chlorophyll d-binding protein 3 (PcbA)


Mass: 38707.781 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6I0
#20: Protein High light inducible protein / Light harvesting chlorophyll d-binding protein 4 (PcbC)


Mass: 37967.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C3E6

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Protein / Protein/peptide / Sugars , 3 types, 8 molecules EeGg

#17: Protein/peptide Unknown protein


Mass: 3507.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria)
#27: 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
#5: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V / PsbE


Mass: 9495.788 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6T2

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Non-polymers , 11 types, 308 molecules

#21: Chemical...
ChemComp-CL7 / CHLOROPHYLL D


Mass: 895.462 Da / Num. of mol.: 212 / Source method: obtained synthetically / Formula: C54H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#23: 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.: 22 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#24: 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.: 14 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#25: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#26: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#28: 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
#29: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#30: 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
#31: 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
#32: Chemical...
ChemComp-ZEX / (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C40H56O2 / 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: PSII-Pcb Dimer of Acaryochloris Marina / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL
Source (natural)Organism: Acaryochloris marina MBIC11017 (bacteria)
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132346 / Symmetry type: POINT

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