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- PDB-7dwq: Photosystem I from a chlorophyll d-containing cyanobacterium Acar... -

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Basic information

Entry
Database: PDB / ID: 7dwq
TitlePhotosystem I from a chlorophyll d-containing cyanobacterium Acaryochloris marina
Components
  • (Photosystem I P740 chlorophyll a apoprotein ...) x 2
  • (Photosystem I protein ...) x 4
  • (Photosystem I reaction center subunit ...) x 3
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem I / reaction center / cryo-EM / cyanobacteria
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily ...Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Chem-8CT / CHLOROPHYLL D / CHLOROPHYLL D ISOMER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 ...Chem-8CT / CHLOROPHYLL D / CHLOROPHYLL D ISOMER / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit II / Photosystem I iron-sulfur center
Similarity search - Component
Biological speciesAcaryochloris marina MBIC11017 (bacteria)
Acaryochloris marinan MBIC11017 (bacteria)
Acaryochloris marina MBIC 11017 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen, J.H. / Zhang, X. / Shen, J.R.
CitationJournal: J Integr Plant Biol / Year: 2021
Title: A unique photosystem I reaction center from a chlorophyll d-containing cyanobacterium Acaryochloris marina.
Authors: Caihuang Xu / Qingjun Zhu / Jing-Hua Chen / Liangliang Shen / Xiaohan Yi / Zihui Huang / Wenda Wang / Min Chen / Tingyun Kuang / Jian-Ren Shen / Xing Zhang / Guangye Han /
Abstract: Photosystem I (PSI) is a large protein supercomplex that catalyzes the light-dependent oxidation of plastocyanin (or cytochrome c ) and the reduction of ferredoxin. This catalytic reaction is ...Photosystem I (PSI) is a large protein supercomplex that catalyzes the light-dependent oxidation of plastocyanin (or cytochrome c ) and the reduction of ferredoxin. This catalytic reaction is realized by a transmembrane electron transfer chain consisting of primary electron donor (a special chlorophyll (Chl) pair) and electron acceptors A , A , and three Fe S clusters, F , F , and F . Here we report the PSI structure from a Chl d-dominated cyanobacterium Acaryochloris marina at 3.3 Å resolution obtained by single-particle cryo-electron microscopy. The A. marina PSI exists as a trimer with three identical monomers. Surprisingly, the structure reveals a unique composition of electron transfer chain in which the primary electron acceptor A is composed of two pheophytin a rather than Chl a found in any other well-known PSI structures. A novel subunit Psa27 is observed in the A. marina PSI structure. In addition, 77 Chls, 13 α-carotenes, two phylloquinones, three Fe-S clusters, two phosphatidyl glycerols, and one monogalactosyl-diglyceride were identified in each PSI monomer. Our results provide a structural basis for deciphering the mechanism of photosynthesis in a PSI complex with Chl d as the dominating pigments and absorbing far-red light.
History
DepositionJan 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
D: Photosystem I protein PsaD
A: Photosystem I P740 chlorophyll a apoprotein A1
B: Photosystem I P740 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
E: Photosystem I reaction center subunit IV
F: Photosystem I protein PsaF
J: Photosystem I reaction center subunit IX
L: Photosystem I protein PsaL
M: Photosystem I reaction center subunit XII
W: Photosystem I protein Psa27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,977110
Polymers245,11610
Non-polymers81,862100
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area53370 Å2
ΔGint-293 kcal/mol
Surface area77890 Å2

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Components

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Photosystem I protein ... , 4 types, 4 molecules DFLW

#1: Protein Photosystem I protein PsaD /


Mass: 15114.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 / References: UniProt: B0C8F1
#6: Protein Photosystem I protein PsaF /


Mass: 17844.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 / References: UniProt: B0C7S7
#8: Protein Photosystem I protein PsaL /


Mass: 15349.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acaryochloris marina MBIC 11017 (bacteria)
Strain: MBIC 11017 / References: UniProt: B0C7S4
#10: Protein/peptide Photosystem I protein Psa27 /


Mass: 3648.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017

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Photosystem I P740 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#2: Protein Photosystem I P740 chlorophyll a apoprotein A1 / / PsaA


Mass: 83470.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 / References: UniProt: B0C474, photosystem I
#3: Protein Photosystem I P740 chlorophyll a apoprotein A2 / / PsaB


Mass: 82210.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 / References: UniProt: B0C475, photosystem I

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Protein , 1 types, 1 molecules C

#4: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8825.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acaryochloris marinan MBIC11017 (bacteria)
Strain: MBIC 11017 / References: UniProt: B0CB42, photosystem I

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Photosystem I reaction center subunit ... , 3 types, 3 molecules EJM

#5: Protein Photosystem I reaction center subunit IV /


Mass: 9560.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 / References: UniProt: B0C5D5
#7: Protein Photosystem I reaction center subunit IX /


Mass: 5900.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acaryochloris marina MBIC 11017 (bacteria)
Strain: MBIC 11017 / References: UniProt: B0C7S6
#9: Protein/peptide Photosystem I reaction center subunit XII /


Mass: 3190.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017

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Non-polymers , 8 types, 100 molecules

#11: Chemical...
ChemComp-CL7 / CHLOROPHYLL D / Chlorophyll d


Mass: 895.462 Da / Num. of mol.: 76 / Source method: obtained synthetically / Formula: C54H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#14: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#15: Chemical ChemComp-G9R / CHLOROPHYLL D ISOMER


Mass: 895.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#17: 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.: 13 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10 / 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: Photosystem I from a chlorophyll d-containing cyanobacterium Acaryochloris marina
Type: COMPLEX / Entity ID: #1-#10 / 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
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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 FIELDBright-field microscopy / Nominal magnification: 22500 X / Calibrated magnification: 38244 X / Nominal defocus max: 3000 nm / Nominal defocus min: 2500 nm / Calibrated defocus min: 2500 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 47 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 4 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEM3.8image acquisition
11cryoSPARC2.12final Euler assignment
12cryoSPARC2.12classification
13cryoSPARC2.123D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1523356 / Details: raw particles
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 240880 / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00321076
ELECTRON MICROSCOPYf_angle_d1.00429918
ELECTRON MICROSCOPYf_dihedral_angle_d16.4432927
ELECTRON MICROSCOPYf_chiral_restr0.0432620
ELECTRON MICROSCOPYf_plane_restr0.0043939

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