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- PDB-8gwa: Structure of the intact photosynthetic light-harvesting antenna-r... -

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Entry
Database: PDB / ID: 8gwa
TitleStructure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium
Components
  • (Photosystem P840 reaction ...) x 2
  • Bacteriochlorophyll ...
  • Cytochrome c
  • P840 reaction center 17 kDa protein
  • Ric1 protein
  • unkown protein
KeywordsPHOTOSYNTHESIS / Green sulfur bacterium / Reaction center / FMO protein / 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
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / CARDIOLIPIN / 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 / CARDIOLIPIN / 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 / P840 reaction center 17 kDa protein / Ric1 protein
Similarity search - Component
Biological speciesChlorobaculum tepidum TLS (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsChen, J.H. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Integr Plant Biol / Year: 2023
Title: Cryo-electron microscopy structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium.
Authors: Jing-Hua Chen / Weiwei Wang / Chen Wang / Tingyun Kuang / Jian-Ren Shen / Xing Zhang /
Abstract: The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna-Matthews-Olson ...The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna-Matthews-Olson (FMO). Functionally, FMO transfers the absorbed energy from a huge peripheral light-harvesting antenna named chlorosome to the RC core where charge separation occurs. In vivo, one RC was found to bind two FMOs, however, the intact structure of RCC as well as the energy transfer mechanism within RCC remain to be clarified. Here we report a structure of intact RCC which contains a RC core and two FMO trimers from a thermophilic green sulfur bacterium Chlorobaculum tepidum at 2.9 Å resolution by cryo-electron microscopy. The second FMO trimer is attached at the cytoplasmic side asymmetrically relative to the first FMO trimer reported previously. We also observed two new subunits (PscE and PscF) and the N-terminal transmembrane domain of a cytochrome-containing subunit (PscC) in the structure. These two novel subunits possibly function to facilitate the binding of FMOs to RC core and to stabilize the whole complex. A new bacteriochlorophyll (numbered as 816) was identified at the interspace between PscF and PscA-1, causing an asymmetrical energy transfer from the two FMO trimers to RC core. Based on the structure, we propose an energy transfer network within this photosynthetic apparatus.
History
DepositionSep 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 2.0Dec 21, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Data processing / Derived calculations / Experimental preparation / Refinement description / Structure summary
Category: atom_site / em_3d_reconstruction ...atom_site / em_3d_reconstruction / em_entity_assembly_molwt / em_image_recording / em_imaging / em_imaging_optics / em_particle_selection / em_single_particle_entity / em_software / em_vitrification / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine_ls_restr / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _em_3d_reconstruction.num_class_averages / _em_3d_reconstruction.num_particles / _em_image_recording.average_exposure_time / _em_image_recording.avg_electron_dose_per_image / _em_image_recording.num_grids_imaged / _em_image_recording.num_real_images / _em_imaging.alignment_procedure / _em_imaging.calibrated_magnification / _em_imaging.cryogen / _em_imaging.nominal_magnification / _em_imaging.recording_temperature_maximum / _em_imaging.recording_temperature_minimum / _em_imaging.specimen_holder_model / _em_software.name / _em_software.version / _em_vitrification.chamber_temperature / _em_vitrification.cryogen_name / _em_vitrification.humidity / _em_vitrification.instrument / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _refine_ls_restr.dev_ideal / _struct_asym.entity_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet.number_strands
Description: Model orientation/position / Details: The model does not fit the map well / Provider: author / Type: Coordinate replacement
Revision 2.1Jan 11, 2023Group: Database references / Category: citation / Item: _citation.title
Revision 2.2Feb 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Bacteriochlorophyll a protein
3: Bacteriochlorophyll a protein
2: 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
4: Bacteriochlorophyll a protein
6: Bacteriochlorophyll a protein
5: Bacteriochlorophyll a protein
E: unkown protein
F: Ric1 protein
C: Cytochrome c
c: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)592,513117
Polymers502,31114
Non-polymers90,202103
Water0
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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Bacteriochlorophyll ... , 1 types, 6 molecules 132465

#1: Protein
Bacteriochlorophyll a protein / Bacteriochlorophyll / 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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Protein , 4 types, 5 molecules DEFCc

#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 TLS (bacteria) / Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / References: UniProt: Q8KEP5
#5: Protein unkown protein


Mass: 4954.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum TLS (bacteria)
#6: Protein Ric1 protein


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
#7: 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

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

#3: Protein Photosystem P840 reaction center iron-sulfur protein


Mass: 23383.096 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
#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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Non-polymers , 10 types, 103 molecules

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


Mass: 911.504 Da / Num. of mol.: 73 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#9: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#10: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#11: 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
#12: 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
#13: 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.: 4 / Source method: obtained synthetically / Formula: C58H86O7
#14: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#15: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#17: 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

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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: GsbRC-2FMO complex / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlorobaculum tepidum TLS (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: 130000 X / Calibrated magnification: 152200 X / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 90 K / Temperature (min): 80 K
Image recordingAverage exposure time: 8 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2297
EM imaging opticsEnergyfilter name: TFS Selectris / Chromatic aberration corrector: 2.7mm / Energyfilter slit width: 10 eV / Spherical aberration corrector: 2.7mm

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARC3particle selection
4cryoSPARC3CTF correction
10cryoSPARC3initial Euler assignment
11cryoSPARC3final Euler assignment
12cryoSPARC3classification
13cryoSPARC33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1961370
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227038 / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00339180
ELECTRON MICROSCOPYf_angle_d0.7254253
ELECTRON MICROSCOPYf_dihedral_angle_d13.126962
ELECTRON MICROSCOPYf_chiral_restr0.0445345
ELECTRON MICROSCOPYf_plane_restr0.0056024

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