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- PDB-6vpv: Trimeric Photosystem I from the High-Light Tolerant Cyanobacteria... -

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Basic information

Entry
Database: PDB / ID: 6vpv
TitleTrimeric Photosystem I from the High-Light Tolerant Cyanobacteria Cyanobacterium Aponinum
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 7
  • PSI-F
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem I / Membrane Protein / PSI
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 / membrane => GO:0016020 / photosynthesis / 4 iron, 4 sulfur cluster binding ...: / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / membrane => GO:0016020 / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI ...Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / 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 reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / 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
BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit XI ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit XI / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit II / Photosystem I iron-sulfur center / Photosystem I reaction center subunit IV / PSI-F / Photosystem I reaction center subunit IX / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesCyanobacterium aponinum 0216 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsDobson, Z. / Toporik, H. / Vaughn, N. / Lin, S. / Williams, D. / Fromme, P. / Mazor, Y.
CitationJournal: Elife / Year: 2021
Title: The structure of photosystem I from a high-light-tolerant cyanobacteria.
Authors: Zachary Dobson / Safa Ahad / Jackson Vanlandingham / Hila Toporik / Natalie Vaughn / Michael Vaughn / Dewight Williams / Michael Reppert / Petra Fromme / Yuval Mazor /
Abstract: Photosynthetic organisms have adapted to survive a myriad of extreme environments from the earth's deserts to its poles, yet the proteins that carry out the light reactions of photosynthesis are ...Photosynthetic organisms have adapted to survive a myriad of extreme environments from the earth's deserts to its poles, yet the proteins that carry out the light reactions of photosynthesis are highly conserved from the cyanobacteria to modern day crops. To investigate adaptations of the photosynthetic machinery in cyanobacteria to excessive light stress, we isolated a new strain of cyanobacteria, 0216, from the extreme light environment of the Sonoran Desert. Here we report the biochemical characterization and the 2.7 Å resolution structure of trimeric photosystem I from this high-light-tolerant cyanobacterium. The structure shows a new conformation of the PsaL C-terminus that supports trimer formation of cyanobacterial photosystem I. The spectroscopic analysis of this photosystem I revealed a decrease in far-red absorption, which is attributed to a decrease in the number of long- wavelength chlorophylls. Using these findings, we constructed two chimeric PSIs in sp. PCC 6803 demonstrating how unique structural features in photosynthetic complexes can change spectroscopic properties, allowing organisms to thrive under different environmental stresses.
History
DepositionFeb 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: PSI-F
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
a: Photosystem I P700 chlorophyll a apoprotein A1
b: Photosystem I P700 chlorophyll a apoprotein A2
c: Photosystem I iron-sulfur center
d: Photosystem I reaction center subunit II
e: Photosystem I reaction center subunit IV
f: PSI-F
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
k: Photosystem I reaction center subunit PsaK
l: Photosystem I reaction center subunit XI
m: Photosystem I reaction center subunit XII
1: Photosystem I P700 chlorophyll a apoprotein A1
2: Photosystem I P700 chlorophyll a apoprotein A2
3: Photosystem I iron-sulfur center
4: Photosystem I reaction center subunit II
5: Photosystem I reaction center subunit IV
6: PSI-F
7: Photosystem I reaction center subunit VIII
8: Photosystem I reaction center subunit IX
9: Photosystem I reaction center subunit PsaK
0: Photosystem I reaction center subunit XI
z: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,051,662417
Polymers742,34033
Non-polymers309,323384
Water00
1


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

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 6 molecules Aa1Bb2

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PsaA


Mass: 81754.039 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cyanobacterium aponinum 0216 (bacteria) / Strain: 0216 / References: UniProt: A0A2G3P9X3, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 81865.945 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cyanobacterium aponinum 0216 (bacteria) / Strain: 0216 / References: UniProt: K9Z2J7, photosystem I

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Protein , 2 types, 6 molecules Cc3Ff6

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


Mass: 8692.039 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cyanobacterium aponinum 0216 (bacteria) / Strain: 0216 / References: UniProt: A0A2G3PD04, photosystem I
#6: Protein PSI-F / Photosystem I reaction center subunit III


Mass: 15665.845 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cyanobacterium aponinum 0216 (bacteria) / Strain: 0216 / References: UniProt: A0A2G3PEV5

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Photosystem I reaction center subunit ... , 7 types, 21 molecules Dd4Ee5Ii7Jj8Kk9Ll0Mmz

#4: Protein Photosystem I reaction center subunit II


Mass: 15647.748 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cyanobacterium aponinum 0216 (bacteria) / Strain: 0216 / References: UniProt: A0A2G3PAQ0
#5: Protein Photosystem I reaction center subunit IV


Mass: 7634.534 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cyanobacterium aponinum 0216 (bacteria) / Strain: 0216 / References: UniProt: A0A2G3PEU8
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 3913.726 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cyanobacterium aponinum 0216 (bacteria) / Strain: 0216 / References: UniProt: K9Z9J3
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4354.158 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cyanobacterium aponinum 0216 (bacteria) / Strain: 0216 / References: UniProt: A0A2G3PEV6
#9: Protein Photosystem I reaction center subunit PsaK / Photosystem I subunit X


Mass: 7860.323 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cyanobacterium aponinum 0216 (bacteria) / Strain: 0216 / References: UniProt: A0A2G3P6W6
#10: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16779.295 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cyanobacterium aponinum 0216 (bacteria) / Strain: 0216 / References: UniProt: A0A2G3P7D5
#11: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3278.920 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cyanobacterium aponinum 0216 (bacteria) / Strain: 0216 / References: UniProt: A0A2G3PA81

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Non-polymers , 8 types, 384 molecules

#12: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#13: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 285 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H46O2
#15: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#16: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 69 / Source method: obtained synthetically / Formula: C40H56
#17: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#18: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10
#19: 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.: 3 / Source method: obtained synthetically / Formula: C41H78O12S

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Details

Has ligand of interestN
Has protein modificationY

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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: Trimeric PSI from a High Light tolerant cyanobacteria, Cyanobacterium aponinum
Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL
Source (natural)Organism: Cyanobacterium aponinum 0216 (bacteria) / Strain: 216
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
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
Image recordingElectron dose: 1.53 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
10RELION3.0.7initial Euler assignment
11RELION3.0.7final Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75290 / Symmetry type: POINT

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