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- PDB-6k61: Cryo-EM structure of the tetrameric photosystem I from a heterocy... -

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Entry
Database: PDB / ID: 6k61
TitleCryo-EM structure of the tetrameric photosystem I from a heterocyst-forming cyanobacterium Anabaena sp. PCC7120
Components(Photosystem I ...) x 12
KeywordsPHOTOSYNTHESIS / Photosystem I / PSI / PCC7120
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 / oxidoreductase activity ...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 / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Single helix bin / 4Fe-4S dicluster domain ...Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Single helix bin / 4Fe-4S dicluster domain / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / SH3 type barrels. - #50 / 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 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 / Alpha-Beta Plaits - #20 / 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 PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / 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 / Helicase, Ruva Protein; domain 3 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
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 iron-sulfur center / Photosystem I reaction center subunit VIII ...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 iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit III / Photosystem I P700 chlorophyll a apoprotein A2 1 / Photosystem I 4.8 kDa protein / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit PsaK 1 / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsZheng, L. / Li, Y. / Li, X. / Zhong, Q. / Li, N. / Zhang, K. / Zhang, Y. / Chu, H. / Ma, C. / Li, G. ...Zheng, L. / Li, Y. / Li, X. / Zhong, Q. / Li, N. / Zhang, K. / Zhang, Y. / Chu, H. / Ma, C. / Li, G. / Zhao, J. / Gao, N.
Funding support1items
OrganizationGrant numberCountry
National Science Foundation (China)
CitationJournal: Nat Plants / Year: 2019
Title: Structural and functional insights into the tetrameric photosystem I from heterocyst-forming cyanobacteria.
Authors: Lvqin Zheng / Yanbing Li / Xiying Li / Qinglu Zhong / Ningning Li / Kun Zhang / Yuebin Zhang / Huiying Chu / Chengying Ma / Guohui Li / Jindong Zhao / Ning Gao /
Abstract: Two large protein-cofactor complexes, photosystem I and photosystem II, are the central components of photosynthesis in the thylakoid membranes. Here, we report the 2.37-Å structure of a tetrameric ...Two large protein-cofactor complexes, photosystem I and photosystem II, are the central components of photosynthesis in the thylakoid membranes. Here, we report the 2.37-Å structure of a tetrameric photosystem I complex from a heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. Four photosystem I monomers, organized in a dimer of dimer, form two distinct interfaces that are largely mediated by specifically orientated polar lipids, such as sulfoquinovosyl diacylglycerol. The structure depicts a more closely connected network of chlorophylls across monomer interfaces than those seen in trimeric PSI from thermophilic cyanobacteria, possibly allowing a more efficient energy transfer between monomers. Our physiological data also revealed a functional link of photosystem I oligomerization to cyclic electron flow and thylakoid membrane organization.
History
DepositionMay 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
X: Photosystem I 4.8 kDa protein
B: Photosystem I P700 chlorophyll a apoprotein A2 1
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK 1
I: Photosystem I reaction center subunit VIII
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
a: Photosystem I P700 chlorophyll a apoprotein A1
x: Photosystem I 4.8 kDa protein
b: Photosystem I P700 chlorophyll a apoprotein A2 1
c: Photosystem I iron-sulfur center
d: Photosystem I reaction center subunit II
e: Photosystem I reaction center subunit IV
f: Photosystem I reaction center subunit III
j: Photosystem I reaction center subunit IX
k: Photosystem I reaction center subunit PsaK 1
i: Photosystem I reaction center subunit VIII
l: Photosystem I reaction center subunit XI
m: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)733,164283
Polymers524,91324
Non-polymers208,251259
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, negative staining
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area418190 Å2
ΔGint-3250 kcal/mol
Surface area124020 Å2

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Components

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Photosystem I ... , 12 types, 24 molecules AaXxBbCcDdEeFfJjKkIiLlMm

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


Mass: 83289.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58576, photosystem I
#2: Protein/peptide Photosystem I 4.8 kDa protein


Mass: 4872.792 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58566
#3: Protein Photosystem I P700 chlorophyll a apoprotein A2 1 / PsaB 1


Mass: 83457.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58565, photosystem I
#4: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8825.206 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P0A410, photosystem I
#5: Protein Photosystem I reaction center subunit II


Mass: 15176.240 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58573
#6: Protein Photosystem I reaction center subunit IV


Mass: 7897.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58575
#7: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 17850.568 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58564
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 5499.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58568
#9: Protein Photosystem I reaction center subunit PsaK 1 / Photosystem I subunit X 1


Mass: 8852.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58583
#10: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 5066.925 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58560
#11: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 18130.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: P58577
#12: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3538.204 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / References: UniProt: Q8YNB0

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Non-polymers , 8 types, 259 molecules

#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 188 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#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.: 4 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / 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: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Photosystem I complex of cyanobacterium Anabaena sp. PCC 7120
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#12 / Source: NATURAL
Molecular weightValue: 1.3 MDa
Source (natural)Organism: Nostoc sp. PCC 7120 (bacteria)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 FIELD / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71600 / Symmetry type: POINT

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