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- PDB-7ueb: Photosynthetic assembly of Chlorobaculum tepidum (RC-FMO2) -

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Basic information

Entry
Database: PDB / ID: 7ueb
TitlePhotosynthetic assembly of Chlorobaculum tepidum (RC-FMO2)
Components
  • (Photosystem P840 reaction ...) x 2
  • Bacteriochlorophyll ...
  • Cytochrome c
  • P840 reaction center 17 kDa protein
  • PscE
  • PscF
KeywordsPHOTOSYNTHESIS / FMO / reaction center / single-particle cryo-EM / bacteriochlorophyll / electron transport chain / energy transfer
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
Proteolipid membrane potential modulator / Proteolipid membrane potential modulator / 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 ...Proteolipid membrane potential modulator / Proteolipid membrane potential modulator / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / Chem-F26 / Chem-F39 / Chlorophyll A ester / Bacteriochlorophyll A isomer / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / IRON/SULFUR CLUSTER / Cytochrome c / Bacteriochlorophyll a protein ...BACTERIOCHLOROPHYLL A / Chem-F26 / Chem-F39 / Chlorophyll A ester / Bacteriochlorophyll A isomer / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / IRON/SULFUR CLUSTER / Cytochrome c / Bacteriochlorophyll a protein / Photosystem P840 reaction center, large subunit / Photosystem P840 reaction center iron-sulfur protein / Uncharacterized protein / P840 reaction center 17 kDa protein / Ric1 protein
Similarity search - Component
Biological speciesChlorobaculum tepidum TLS (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsPuskar, R. / Truong, C.D. / Swain, K. / Li, S. / Cheng, K.-W. / Wang, T.Y. / Poh, Y.-P. / Liu, H. / Chou, T.-F. / Nannenga, B. / Chiu, P.-L.
Funding support United States, 2items
OrganizationGrant numberCountry
Other governmentW911NF2010321
National Science Foundation (NSF, United States)NSF MRI 1531991 United States
CitationJournal: Nat Commun / Year: 2022
Title: Molecular asymmetry of a photosynthetic supercomplex from green sulfur bacteria.
Authors: Ryan Puskar / Chloe Du Truong / Kyle Swain / Saborni Chowdhury / Ka-Yi Chan / Shan Li / Kai-Wen Cheng / Ting Yu Wang / Yu-Ping Poh / Yuval Mazor / Haijun Liu / Tsui-Fen Chou / Brent L Nannenga / Po-Lin Chiu /
Abstract: The photochemical reaction center (RC) features a dimeric architecture for charge separation across the membrane. In green sulfur bacteria (GSB), the trimeric Fenna-Matthews-Olson (FMO) complex ...The photochemical reaction center (RC) features a dimeric architecture for charge separation across the membrane. In green sulfur bacteria (GSB), the trimeric Fenna-Matthews-Olson (FMO) complex mediates the transfer of light energy from the chlorosome antenna complex to the RC. Here we determine the structure of the photosynthetic supercomplex from the GSB Chlorobaculum tepidum using single-particle cryogenic electron microscopy (cryo-EM) and identify the cytochrome c subunit (PscC), two accessory protein subunits (PscE and PscF), a second FMO trimeric complex, and a linker pigment between FMO and the RC core. The protein subunits that are assembled with the symmetric RC core generate an asymmetric photosynthetic supercomplex. One linker bacteriochlorophyll (BChl) is located in one of the two FMO-PscA interfaces, leading to differential efficiencies of the two energy transfer branches. The two FMO trimeric complexes establish two different binding interfaces with the RC cytoplasmic surface, driven by the associated accessory subunits. This structure of the GSB photosynthetic supercomplex provides mechanistic insight into the light excitation energy transfer routes and a possible evolutionary transition intermediate of the bacterial photosynthetic supercomplex from the primitive homodimeric RC.
History
DepositionMar 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: 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 / _citation_author.name
Revision 1.2Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photosystem P840 reaction center, large subunit
a: Photosystem P840 reaction center, large subunit
B: Photosystem P840 reaction center iron-sulfur protein
C: Cytochrome c
c: Cytochrome c
D: P840 reaction center 17 kDa protein
E: PscE
F: PscF
U: Bacteriochlorophyll a protein
V: Bacteriochlorophyll a protein
W: Bacteriochlorophyll a protein
X: Bacteriochlorophyll a protein
Y: Bacteriochlorophyll a protein
Z: Bacteriochlorophyll a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)593,506120
Polymers504,20514
Non-polymers89,301106
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, gel filtration
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 , 4 types, 5 molecules CcDEF

#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
#5: Protein PscE


Mass: 6690.926 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: Q8KDI3
#6: Protein PscF


Mass: 6227.533 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: Q8KG87

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Bacteriochlorophyll ... , 1 types, 6 molecules UVWXYZ

#7: 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, 106 molecules

#8: 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
#9: Chemical
ChemComp-G2O / Chlorophyll A ester


Mass: 891.473 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H70MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 73 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#11: 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.: 3 / Source method: obtained synthetically / Formula: C58H86O7 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-F26 / 2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E,19E)-3,7,12,16,20,24-hexamethylpentacosa-1,3,5,7,9,11,13,15,17,19,23-undecaenyl]-1,3,4-trimethyl-benzene


Mass: 532.841 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H52 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#14: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#15: 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
#16: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / 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: Photosynthetic assembly (RC-FMO2) / Type: COMPLEX
Details: Photosynthetic assembly from Chlorobaculum tepidum (RC-FMO2)
Entity ID: #1-#7 / Source: NATURAL
Molecular weightValue: 0.504 MDa / Experimental value: NO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria) / Cellular location: Membrane
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-ClTris-Cl1
2200 mMNaClSodium chlorideNaClSodium chloride1
30.17 mMDDMDDM1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen 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 FIELDBright-field microscopy / Calibrated magnification: 47259 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 45.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 32898
Image scansSampling size: 5 µm / Movie frames/image: 30

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Processing

EM software
IDNameVersionCategory
1Topaz0.2.5particle selection
2SerialEM3.9image acquisition
4cryoSPARC3.3.1CTF correction
7UCSF Chimera1.16model fitting
9cryoSPARC3.3.1initial Euler assignment
10cryoSPARC3.3.1final Euler assignment
11cryoSPARC3.3.1classification
12cryoSPARC3.3.13D reconstruction
13PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1938908
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157486 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 44.07 / Protocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 6M32

6m32


Accession code: 6M32 / Source name: PDB / Type: experimental model

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