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- PDB-7eqd: STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOSPIRILLU... -

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Basic information

Entry
Database: PDB / ID: 7eqd
TitleSTRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOSPIRILLUM RUBRUM
Components
  • (Light-harvesting protein B-870 ...) x 2
  • (Reaction center protein ...) x 2
  • Photoreaction center protein H
KeywordsPHOTOSYNTHESIS / LH1-RC COMPLEX / PURPLE BACTERIA
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane / metal ion binding / plasma membrane
Similarity search - Function
Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex ...Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Trans-Geranyl BACTERIOCHLOROPHYLL A / Trans-Geranyl BACTERIOPHEOPHYTIN A / CARDIOLIPIN / SPIRILLOXANTHIN / : / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGV / Chem-RQ0 / UBIQUINONE-10 / Light-harvesting protein B-870 alpha chain ...Trans-Geranyl BACTERIOCHLOROPHYLL A / Trans-Geranyl BACTERIOPHEOPHYTIN A / CARDIOLIPIN / SPIRILLOXANTHIN / : / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGV / Chem-RQ0 / UBIQUINONE-10 / Light-harvesting protein B-870 alpha chain / Reaction center protein L chain / Light-harvesting protein B-870 beta chain / Reaction center protein M chain / Photoreaction center protein H
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsTani, K. / Kanno, R. / Ji, X.-C. / Yu, L.-J. / Hall, M. / Kimura, Y. / Madigan, M.T. / Mizoguchi, A. / Humbel, B.M. / Wang-Otomo, Z.-Y.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101116 Japan
Japan Society for the Promotion of Science (JSPS)JP16H04174 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05153 Japan
Japan Society for the Promotion of Science (JSPS)20H05086 Japan
Japan Society for the Promotion of Science (JSPS)20H02856 Japan
CitationJournal: Biochemistry / Year: 2021
Title: Cryo-EM Structure of the Photosynthetic LH1-RC Complex from .
Authors: Kazutoshi Tani / Ryo Kanno / Xuan-Cheng Ji / Malgorzata Hall / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Zheng-Yu Wang-Otomo /
Abstract: () is one of the most widely used model organisms in bacterial photosynthesis. This purple phototroph is characterized by the presence of both rhodoquinone (RQ) and ubiquinone as electron carriers ... () is one of the most widely used model organisms in bacterial photosynthesis. This purple phototroph is characterized by the presence of both rhodoquinone (RQ) and ubiquinone as electron carriers and bacteriochlorophyll (BChl) esterified at the propionic acid side chain by geranylgeraniol (BChl ) instead of phytol. Despite intensive efforts, the structure of the light-harvesting-reaction center (LH1-RC) core complex from remains at low resolutions. Using cryo-EM, here we present a robust new view of the LH1-RC at 2.76 Å resolution. The LH1 complex forms a closed, slightly elliptical ring structure with 16 αβ-polypeptides surrounding the RC. Our biochemical analysis detected RQ molecules in the purified LH1-RC, and the cryo-EM density map specifically positions RQ at the Q site in the RC. The geranylgeraniol side chains of BChl coordinated by LH1 β-polypeptides exhibit a highly homologous tail-up conformation that allows for interactions with the bacteriochlorin rings of nearby LH1 α-associated BChls . The structure also revealed key protein-protein interactions in both N- and C-terminal regions of the LH1 αβ-polypeptides, mainly within a face-to-face structural subunit. Our high-resolution LH1-RC structure provides new insight for evaluating past experimental and computational results obtained with this old organism over many decades and lays the foundation for more detailed exploration of light-energy conversion, quinone transport, and structure-function relationships in this pigment-protein complex.
History
DepositionMay 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_validate_chiral
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 / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Photoreaction center protein H
A: Light-harvesting protein B-870 alpha chain
B: Light-harvesting protein B-870 beta chain
D: Light-harvesting protein B-870 alpha chain
E: Light-harvesting protein B-870 beta chain
F: Light-harvesting protein B-870 alpha chain
G: Light-harvesting protein B-870 beta chain
I: Light-harvesting protein B-870 alpha chain
J: Light-harvesting protein B-870 beta chain
K: Light-harvesting protein B-870 alpha chain
N: Light-harvesting protein B-870 beta chain
O: Light-harvesting protein B-870 alpha chain
P: Light-harvesting protein B-870 beta chain
Q: Light-harvesting protein B-870 alpha chain
R: Light-harvesting protein B-870 beta chain
S: Light-harvesting protein B-870 alpha chain
T: Light-harvesting protein B-870 beta chain
U: Light-harvesting protein B-870 alpha chain
V: Light-harvesting protein B-870 beta chain
W: Light-harvesting protein B-870 alpha chain
X: Light-harvesting protein B-870 beta chain
Y: Light-harvesting protein B-870 alpha chain
Z: Light-harvesting protein B-870 beta chain
1: Light-harvesting protein B-870 alpha chain
2: Light-harvesting protein B-870 beta chain
3: Light-harvesting protein B-870 alpha chain
4: Light-harvesting protein B-870 beta chain
5: Light-harvesting protein B-870 alpha chain
6: Light-harvesting protein B-870 beta chain
7: Light-harvesting protein B-870 alpha chain
8: Light-harvesting protein B-870 beta chain
9: Light-harvesting protein B-870 alpha chain
0: Light-harvesting protein B-870 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,827127
Polymers305,20535
Non-polymers69,62292
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area176210 Å2
ΔGint-955 kcal/mol
Surface area88220 Å2

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Components

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Reaction center protein ... , 2 types, 2 molecules LM

#1: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 30529.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodospirillum rubrum (bacteria) / References: UniProt: P10717
#2: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34103.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1
References: UniProt: Q2RQ26

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Light-harvesting protein B-870 ... , 2 types, 32 molecules ADFIKOQSUWY13579BEGJNPRTVXZ24680

#4: Protein
Light-harvesting protein B-870 alpha chain / Antenna pigment protein alpha chain / LH-1


Mass: 7140.414 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Rhodospirillum rubrum (bacteria) / References: UniProt: P02947
#5: Protein
Light-harvesting protein B-870 beta chain / Antenna pigment protein beta chain / LH-1


Mass: 6155.019 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Source: (natural) Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1) (bacteria)
Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1
References: UniProt: Q2RQ23

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Protein / Sugars , 2 types, 24 molecules H

#10: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Protein Photoreaction center protein H


Mass: 27844.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodospirillum rubrum (bacteria) / References: UniProt: Q7M149

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Non-polymers , 9 types, 69 molecules

#6: Chemical...
ChemComp-07D / Trans-Geranyl BACTERIOCHLOROPHYLL A


Mass: 901.425 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C55H64MgN4O6
#7: Chemical ChemComp-08I / Trans-Geranyl BACTERIOPHEOPHYTIN A


Mass: 879.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H66N4O6
#8: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#9: Chemical ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#11: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#12: Chemical ChemComp-RQ0 / 2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione


Mass: 844.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C58H85NO3 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C42H60O2
#14: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#15: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestY
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: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodospirillum rubrum
Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Rhodospirillum rubrum (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / 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 FIELD / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 30.6 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1EMAN2particle selection
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 262517
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145033 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 60 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 5Y5S

5y5s


Accession code: 5Y5S / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00524076
ELECTRON MICROSCOPYf_angle_d1.00733164
ELECTRON MICROSCOPYf_dihedral_angle_d22.7864656
ELECTRON MICROSCOPYf_chiral_restr0.0553323
ELECTRON MICROSCOPYf_plane_restr0.0054045

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