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- PDB-7z6q: Cryo-EM structure of the whole photosynthetic complex from the gr... -

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Basic information

Entry
Database: PDB / ID: 7z6q
TitleCryo-EM structure of the whole photosynthetic complex from the green sulfur bacteria
Components
  • (Photosystem P840 reaction ...) x 2
  • Bacteriochlorophyll ...
  • Cytochrome c
  • P840 reaction center 17 kDa protein
KeywordsPHOTOSYNTHESIS / reaction centre / electron transport / energy transfer / green sulfur bacterium / membrane protein / light-harvesting protein complex
Function / homology
Function and homology information


thylakoid / bacteriochlorophyll binding / iron-sulfur cluster binding / photosynthesis / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Photosystem P840 reaction-centre, cytochrome c-551 / Photosystem P840 reaction-centre cytochrome c-551 / Photosystem I P840 reaction centre protein PscD / Photosystem P840 reaction centre protein PscD / Bacteriochlorophyll A protein / Bacteriochlorophyll A superfamily / Bacteriochlorophyll A protein / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein ...Photosystem P840 reaction-centre, cytochrome c-551 / Photosystem P840 reaction-centre cytochrome c-551 / Photosystem I P840 reaction centre protein PscD / Photosystem P840 reaction centre protein PscD / Bacteriochlorophyll A protein / Bacteriochlorophyll A superfamily / Bacteriochlorophyll A protein / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / 4Fe-4S dicluster domain / Cytochrome c-like domain superfamily / 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
BACTERIOCHLOROPHYLL A / CHLOROPHYLL A / Chem-F39 / Bacteriochlorophyll A isomer / Chem-IKV / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / IRON/SULFUR CLUSTER / Cytochrome c / Bacteriochlorophyll a protein / Photosystem P840 reaction center, large subunit ...BACTERIOCHLOROPHYLL A / CHLOROPHYLL A / Chem-F39 / Bacteriochlorophyll A isomer / Chem-IKV / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / IRON/SULFUR CLUSTER / Cytochrome c / Bacteriochlorophyll a protein / Photosystem P840 reaction center, large subunit / Photosystem P840 reaction center iron-sulfur protein / P840 reaction center 17 kDa protein
Similarity search - Component
Biological speciesChlorobaculum tepidum TLS (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsXie, H. / Tsiotis, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Cryo-EM structure of the whole photosynthetic reaction center apparatus from the green sulfur bacterium .
Authors: Hao Xie / Alexandros Lyratzakis / Radhika Khera / Myrto Koutantou / Sonja Welsch / Hartmut Michel / Georgios Tsiotis /
Abstract: Light energy absorption and transfer are very important processes in photosynthesis. In green sulfur bacteria light is absorbed primarily by the chlorosomes and its energy is transferred via the ...Light energy absorption and transfer are very important processes in photosynthesis. In green sulfur bacteria light is absorbed primarily by the chlorosomes and its energy is transferred via the Fenna-Matthews-Olson (FMO) proteins to a homodimeric reaction center (RC). Here, we report the cryogenic electron microscopic structure of the intact FMO-RC apparatus from at 2.5 Å resolution. The FMO-RC apparatus presents an asymmetric architecture and contains two FMO trimers that show different interaction patterns with the RC core. Furthermore, the two permanently bound transmembrane subunits PscC, which donate electrons to the special pair, interact only with the two large PscA subunits. This structure fills an important gap in our understanding of the transfer of energy from antenna to the electron transport chain of this RC and the transfer of electrons from reduced sulfur compounds to the special pair.
History
DepositionMar 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem P840 reaction center, large subunit
B: Photosystem P840 reaction center iron-sulfur protein
C: Cytochrome c
D: P840 reaction center 17 kDa protein
E: Bacteriochlorophyll a protein
F: Bacteriochlorophyll a protein
G: Bacteriochlorophyll a protein
H: Bacteriochlorophyll a protein
I: Bacteriochlorophyll a protein
J: Bacteriochlorophyll a protein
a: Photosystem P840 reaction center, large subunit
c: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)569,592103
Polymers491,28712
Non-polymers78,30591
Water18010
1


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

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Components

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Photosystem P840 reaction ... , 2 types, 3 molecules AaB

#1: Protein Photosystem P840 reaction center, large subunit


Mass: 81784.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q8KAY0
#2: Protein Photosystem P840 reaction center iron-sulfur protein


Mass: 23540.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q8KAY1

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Protein , 2 types, 3 molecules CcD

#3: Protein Cytochrome c / / Cytochrome c-z / Cyt c-z / Photosystem P840 reaction center cytochrome c-551


Mass: 22741.779 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: O07091
#4: Protein P840 reaction center 17 kDa protein


Mass: 16633.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q8KEP5

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Bacteriochlorophyll ... , 1 types, 6 molecules EFGHIJ

#5: Protein
Bacteriochlorophyll a protein / Bacteriochlorophyll / BCP / BChl a protein / Fenna-Matthews-Olson protein / FMO protein


Mass: 40343.430 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q46393

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Non-polymers , 9 types, 101 molecules

#6: Chemical ChemComp-GS0 / Bacteriochlorophyll A isomer


Mass: 911.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-F39 / [(2R,3S,4S,5R,6R)-6-[(10E,12E,14E)-2,6,10,14,19,23-hexamethyl-25-(2,3,6-trimethylphenyl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl dodecanoate


Mass: 895.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C58H86O7 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#11: Chemical ChemComp-IKV / [(2~{R})-2-hexadecanoyloxy-3-[(2~{S},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-propyl] hexadecanoate


Mass: 731.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78O10 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / 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 / Feature type: SUBJECT OF INVESTIGATION
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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 P840 reaction center / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightValue: 0.49 MDa / Experimental value: YES
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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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: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
Image scansWidth: 4092 / Height: 5769

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4cryoSPARC3CTF correction
7Coot0.8.9.2model fitting
9PHENIX1.18.2model refinement
10Coot0.8.9.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4791019
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 481095 / Symmetry type: POINT
Atomic model buildingB value: 60
Atomic model building
IDPDB-ID 3D fitting-ID
13ENI

3eni

1
25V8K

5v8k

1

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