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- PDB-7f0l: STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER S... -

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Basic information

Entry
Database: PDB / ID: 7f0l
TitleSTRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES MONOMER
Components
  • (Light-harvesting protein B-875 alpha ...) x 2
  • (Reaction center protein ...) x 2
  • Antenna pigment protein beta chain
  • Photosynthetic reaction center L subunit
  • PufX
  • protein-U
KeywordsPHOTOSYNTHESIS / LH1-RC COMPLEX / PURPLE BACTERIA
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function
Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / 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 ...Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / 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
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / Chem-PGV / SPHEROIDENE / UBIQUINONE-10 / Uncharacterized protein / Uncharacterized protein / Light-harvesting protein B-875 alpha chain / Antenna pigment protein beta chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsTani, K. / Nagashima, V.P. / Kanno, R. / Kawamura, S. / Kikuchi, R. / Ji, X.-C. / Hall, M. / Yu, L.-J. / Kimura, Y. / Madigan, M.T. ...Tani, K. / Nagashima, V.P. / Kanno, R. / Kawamura, S. / Kikuchi, R. / Ji, X.-C. / Hall, M. / Yu, L.-J. / 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: Nat Commun / Year: 2021
Title: A previously unrecognized membrane protein in the Rhodobacter sphaeroides LH1-RC photocomplex.
Authors: Kazutoshi Tani / Kenji V P Nagashima / Ryo Kanno / Saki Kawamura / Riku Kikuchi / Malgorzata Hall / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / ...Authors: Kazutoshi Tani / Kenji V P Nagashima / Ryo Kanno / Saki Kawamura / Riku Kikuchi / Malgorzata Hall / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Zheng-Yu Wang-Otomo /
Abstract: Rhodobacter (Rba.) sphaeroides is the most widely used model organism in bacterial photosynthesis. The light-harvesting-reaction center (LH1-RC) core complex of this purple phototroph is ...Rhodobacter (Rba.) sphaeroides is the most widely used model organism in bacterial photosynthesis. The light-harvesting-reaction center (LH1-RC) core complex of this purple phototroph is characterized by the co-existence of monomeric and dimeric forms, the presence of the protein PufX, and approximately two carotenoids per LH1 αβ-polypeptides. Despite many efforts, structures of the Rba. sphaeroides LH1-RC have not been obtained at high resolutions. Here we report a cryo-EM structure of the monomeric LH1-RC from Rba. sphaeroides strain IL106 at 2.9 Å resolution. The LH1 complex forms a C-shaped structure composed of 14 αβ-polypeptides around the RC with a large ring opening. From the cryo-EM density map, a previously unrecognized integral membrane protein, referred to as protein-U, was identified. Protein-U has a U-shaped conformation near the LH1-ring opening and was annotated as a hypothetical protein in the Rba. sphaeroides genome. Deletion of protein-U resulted in a mutant strain that expressed a much-reduced amount of the dimeric LH1-RC, indicating an important role for protein-U in dimerization of the LH1-RC complex. PufX was located opposite protein-U on the LH1-ring opening, and both its position and conformation differed from that of previous reports of dimeric LH1-RC structures obtained at low-resolution. Twenty-six molecules of the carotenoid spheroidene arranged in two distinct configurations were resolved in the Rba. sphaeroides LH1 and were positioned within the complex to block its channels. Our findings offer an exciting new view of the core photocomplex of Rba. sphaeroides and the connections between structure and function in bacterial photocomplexes in general.
History
DepositionJun 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 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
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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  • Deposited structure unit
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Assembly

Deposited unit
L: Photosynthetic reaction center L subunit
M: Reaction center protein M chain
H: Reaction center protein H chain
A: Light-harvesting protein B-875 alpha chain
B: Antenna pigment protein beta chain
D: Light-harvesting protein B-875 alpha chain
E: Antenna pigment protein beta chain
F: Light-harvesting protein B-875 alpha chain
G: Antenna pigment protein beta chain
I: Light-harvesting protein B-875 alpha chain
J: Antenna pigment protein beta chain
K: Light-harvesting protein B-875 alpha chain
N: Antenna pigment protein beta chain
O: Light-harvesting protein B-875 alpha chain
P: Antenna pigment protein beta chain
Q: Light-harvesting protein B-875 alpha chain
R: Antenna pigment protein beta chain
S: Light-harvesting protein B-875 alpha chain
T: Antenna pigment protein beta chain
V: Light-harvesting protein B-875 alpha chain
W: Antenna pigment protein beta chain
Y: Light-harvesting protein B-875 alpha chain
Z: Antenna pigment protein beta chain
1: Light-harvesting protein B-875 alpha chain
2: Antenna pigment protein beta chain
3: Light-harvesting protein B-875 alpha chain
4: Antenna pigment protein beta chain
5: Light-harvesting protein B-875 alpha chain
6: Antenna pigment protein beta chain
7: Light-harvesting protein B-875 alpha chain
8: Antenna pigment protein beta chain
X: PufX
U: protein-U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,747145
Polymers277,57033
Non-polymers78,178112
Water00
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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Protein , 3 types, 3 molecules LXU

#1: Protein Photosynthetic reaction center L subunit


Mass: 31491.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria)
#7: Protein PufX


Mass: 9017.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: A0A330HGC2
#8: Protein protein-U


Mass: 5555.558 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: A0A3G6WQU3

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

#2: Protein Reaction center protein M chain


Mass: 34543.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria)
#3: Protein Reaction center protein H chain


Mass: 28091.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: WP_069330428.1 / Source: (natural) Rhodobacter sphaeroides (bacteria)

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Light-harvesting protein B-875 alpha ... , 2 types, 14 molecules ADFIKOQSVY1357

#4: Protein
Light-harvesting protein B-875 alpha chain


Mass: 6473.780 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: WP_069330428.1 / Source: (natural) Rhodobacter sphaeroides (bacteria)
#6: Protein Light-harvesting protein B-875 alpha chain / Antenna pigment protein alpha chain / LH-1


Mass: 6445.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P0C0X9

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Protein/peptide / Sugars , 2 types, 38 molecules BEGJNPRTWZ2468

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#5: Protein/peptide
Antenna pigment protein beta chain


Mass: 5592.361 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: Q7B300

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Non-polymers , 8 types, 88 molecules

#9: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#11: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C59H90O4
#12: 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.: 13 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#13: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#14: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#15: Chemical...
ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C41H60O / Feature type: SUBJECT OF INVESTIGATION
#17: 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.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / 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 Rhodobacter sphaeroides monomer
Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Rhodobacter sphaeroides f. sp. denitrificans (bacteria)
Strain: IL106
Buffer solutionpH: 8
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
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 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: 1.275 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
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 551846
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160448 / 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_d0.00724319
ELECTRON MICROSCOPYf_angle_d2.72933239
ELECTRON MICROSCOPYf_dihedral_angle_d16.4679565
ELECTRON MICROSCOPYf_chiral_restr0.0473371
ELECTRON MICROSCOPYf_plane_restr0.0053943

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