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- PDB-6m32: Cryo-EM structure of FMO-RC complex from green sulfur bacteria -

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Basic information

Entry
Database: PDB / ID: 6m32
TitleCryo-EM structure of FMO-RC complex from green sulfur bacteria
Components
  • (Photosystem P840 reaction ...) x 2
  • Bacteriochlorophyll ...
  • P840 reaction center 17 kDa protein
KeywordsPHOTOSYNTHESIS / Photosynthetic reaction center / Green sulfur bacteria / Energy transfer
Function / homology
Function and homology information


thylakoid / bacteriochlorophyll binding / iron-sulfur cluster binding / photosynthesis / membrane / metal ion binding
Similarity search - Function
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 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site ...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 / 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 / Chem-F26 / Chem-F39 / Chlorophyll A ester / Bacteriochlorophyll A isomer / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / IRON/SULFUR CLUSTER / Bacteriochlorophyll a protein / Photosystem P840 reaction center, large subunit ...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 / 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 (bacteria)
Chlorobaculum tepidum TLS (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChen, J.H. / Zhang, X.
CitationJournal: Science / Year: 2020
Title: Architecture of the photosynthetic complex from a green sulfur bacterium.
Authors: Jing-Hua Chen / Hangjun Wu / Caihuang Xu / Xiao-Chi Liu / Zihui Huang / Shenghai Chang / Wenda Wang / Guangye Han / Tingyun Kuang / Jian-Ren Shen / Xing Zhang /
Abstract: The photosynthetic apparatus of green sulfur bacteria (GSB) contains a peripheral antenna chlorosome, light-harvesting Fenna-Matthews-Olson proteins (FMO), and a reaction center (GsbRC). We used cryo- ...The photosynthetic apparatus of green sulfur bacteria (GSB) contains a peripheral antenna chlorosome, light-harvesting Fenna-Matthews-Olson proteins (FMO), and a reaction center (GsbRC). We used cryo-electron microscopy to determine a 2.7-angstrom structure of the FMO-GsbRC supercomplex from The GsbRC binds considerably fewer (bacterio)chlorophylls [(B)Chls] than other known type I RCs do, and the organization of (B)Chls is similar to that in photosystem II. Two BChl layers in GsbRC are not connected by Chls, as seen in other RCs, but associate with two carotenoid derivatives. Relatively long distances of 22 to 33 angstroms were observed between BChls of FMO and GsbRC, consistent with the inefficient energy transfer between these entities. The structure contains common features of both type I and type II RCs and provides insight into the evolution of photosynthetic RCs.
History
DepositionMar 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)380,92674
Polymers324,7737
Non-polymers56,15367
Water0
1


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

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Components

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

#3: 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 (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q8KAY1
#4: 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) / References: UniProt: Q8KAY0

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Bacteriochlorophyll ... / Protein , 2 types, 4 molecules EFGD

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


Mass: 40343.430 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q46393
#2: 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 (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q8KEP5

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Non-polymers , 9 types, 67 molecules

#5: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-GS0 / Bacteriochlorophyll A isomer


Mass: 911.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#8: 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.: 2 / Source method: obtained synthetically / Formula: C40H52
#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
#10: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


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


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H86O10
#12: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#13: Chemical
ChemComp-G2O / Chlorophyll A ester


Mass: 891.473 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H70MgN4O5

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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: FMO-RC of green sulfur bacteria / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen 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 FIELDBright-field microscopy / Nominal magnification: 22500 X / Calibrated magnification: 38244 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 47 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 9156
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 4 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEM3.8image acquisition
4cryoSPARC2.12CTF correction
10cryoSPARC2.12initial Euler assignment
11cryoSPARC2.12final Euler assignment
12cryoSPARC2.12classification
13cryoSPARC2.123D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 3947008 / Details: raw particles
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 268430 / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 44.23 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00524618
ELECTRON MICROSCOPYf_angle_d0.96234250
ELECTRON MICROSCOPYf_dihedral_angle_d16.4998708
ELECTRON MICROSCOPYf_chiral_restr0.1053356
ELECTRON MICROSCOPYf_plane_restr0.0063782

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