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- PDB-6trd: Cryo- EM structure of the Thermosynechococcus elongatus photosyst... -

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Basic information

Entry
Database: PDB / ID: 6trd
TitleCryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of cytochrome c6
Components(Photosystem I ...) x 12
KeywordsPHOTOSYNTHESIS / Photosystem I / P700 / 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 / 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 / membrane
Similarity search - Function
Photosystem I PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / 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 PsaX / Photosystem I PsaX superfamily / PsaX family / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / 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 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 / 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 / Up-down Bundle / Mainly Alpha
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 / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 ...BETA-CAROTENE / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit III / Photosystem I reaction center subunit XII / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit PsaK / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XI / Photosystem I 4.8K protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsKoelsch, A. / Radon, C. / Baumert, A. / Buerger, J. / Mielke, T. / Lisdat, F. / Zouni, A. / Wendler, P.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008/1 Germany
German Research Foundation (DFG)EXC 314/2 Germany
German Federal Ministry for Education and Research031B0557 A+B Germany
CitationJournal: Curr.Opin.Struct.Biol. / Year: 2020
Title: Current limits of structural biology: The transient interaction between cytochrome c6 and photosystem I
Authors: Koelsch, A. / Radon, C. / Golub, M. / Baumert, A. / Burger, J. / Miehlke, T. / Lisdat, F. / Feoktystov, A. / Pieper, J. / Zouni, A. / Wendler, P.
History
DepositionDec 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 2.0Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_validate_chiral
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Apr 9, 2025Data content type: EM metadata
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Group: Data processing / Database references ...Data processing / Database references / Experimental summary / Refinement description
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Category: database_2 / em_3d_fitting_list ...database_2 / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update
Revision 2.1Oct 1, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: em_admin / pdbx_modification_feature ...em_admin / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _em_admin.last_update
Revision 1.2Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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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: Photosystem I reaction center subunit III
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
X: Photosystem I 4.8K protein
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: Photosystem I reaction center subunit III
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
x: Photosystem I 4.8K protein
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: Photosystem I reaction center subunit III
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
y: Photosystem I reaction center subunit XII
z: Photosystem I 4.8K protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,084,613438
Polymers766,63736
Non-polymers317,976402
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area660790 Å2
ΔGint-5099 kcal/mol
Surface area183000 Å2
MethodPISA

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Components

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Photosystem I ... , 12 types, 36 molecules Aa1Bb2Cc3Dd4Ee5Ff6Ii7Jj8Kk9Ll0...

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


Mass: 83267.773 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A405, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 83123.648 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A407, photosystem I
#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8809.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A415, photosystem I
#4: Protein Photosystem I reaction center subunit II / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15389.494 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A420
#5: Protein Photosystem I reaction center subunit IV / Photosystem I 8.1 kDa protein / p30 protein


Mass: 8399.485 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A423
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 15129.358 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A401
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 4325.245 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A427
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4798.708 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A429
#9: Protein Photosystem I reaction center subunit PsaK / Light-harvesting 8.0 kDa polypeptide / Photosystem I subunit X


Mass: 8483.983 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A425
#10: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16287.765 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DGB4
#11: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3426.115 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A403
#12: Protein/peptide Photosystem I 4.8K protein


Mass: 4104.939 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DKP6

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Non-polymers , 9 types, 453 molecules

#13: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


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


Mass: 893.489 Da / Num. of mol.: 288 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#15: 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
#16: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 536.873 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: C40H56
#18: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#19: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#20: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10
#21: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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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: photosystem I / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
10.025 mMTricineTricine1
20.025 mMsodium chlorideNaCl1
30.02 %n-Dodecyl beta-D-maltosideC24H46O111
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Photosystem I was crosslinked with its electron donor cytochrome c6. Crosslinked particles are monodisperse.
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 32 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1.10CTF correction
7Coot0.8.9.1model fitting
9PHENIX1.15model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionDetails: CTFFIND4 was used to estimate contrast transfer function parameters. CTF correction was done in Relion 3.0.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175999 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 1JB0

1jb0


Accession code: 1JB0 / Source name: PDB / Type: experimental model

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