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- PDB-7xxf: Structure of photosynthetic LH1-RC super-complex of Rhodopila glo... -

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Basic information

Entry
Database: PDB / ID: 7xxf
TitleStructure of photosynthetic LH1-RC super-complex of Rhodopila globiformis
Components
  • (Light-harvesting ...) x 3
  • (Photosynthetic reaction center ...Photosynthetic reaction centre) x 2
  • (Reaction center protein ...Photosynthetic reaction centre) x 2
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 / electron transfer activity / membrane => GO:0016020 / iron ion binding ...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 / electron transfer activity / membrane => GO:0016020 / iron ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta 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 / Multiheme cytochrome 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
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / HEME C / Chem-I7D / MENAQUINONE-9 / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PGV / UBIQUINONE-10 ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / HEME C / Chem-I7D / MENAQUINONE-9 / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PGV / UBIQUINONE-10 / Photosynthetic reaction center subunit H / Reaction center protein L chain / Light-harvesting protein / Photosynthetic reaction center cytochrome c subunit / Light-harvesting protein / Reaction center protein M chain
Similarity search - Component
Biological speciesRhodopila globiformis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsTani, K. / Kanno, R. / Kurosawa, K. / Takaichi, S. / Nagashima, K.V.P. / Hall, M. / Yu, L.-J. / Kimura, Y. / Madigan, M.T. / Mizoguchi, A. ...Tani, K. / Kanno, R. / Kurosawa, K. / Takaichi, S. / Nagashima, K.V.P. / 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
Citation
Journal: Commun Biol / Year: 2022
Title: An LH1-RC photocomplex from an extremophilic phototroph provides insight into origins of two photosynthesis proteins.
Authors: Kazutoshi Tani / Ryo Kanno / Keigo Kurosawa / Shinichi Takaichi / Kenji V P Nagashima / Malgorzata Hall / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M ...Authors: Kazutoshi Tani / Ryo Kanno / Keigo Kurosawa / Shinichi Takaichi / Kenji V P Nagashima / Malgorzata Hall / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Zheng-Yu Wang-Otomo /
Abstract: Rhodopila globiformis is the most acidophilic of anaerobic purple phototrophs, growing optimally in culture at pH 5. Here we present a cryo-EM structure of the light-harvesting 1-reaction center (LH1- ...Rhodopila globiformis is the most acidophilic of anaerobic purple phototrophs, growing optimally in culture at pH 5. Here we present a cryo-EM structure of the light-harvesting 1-reaction center (LH1-RC) complex from Rhodopila globiformis at 2.24 Å resolution. All purple bacterial cytochrome (Cyt, encoded by the gene pufC) subunit-associated RCs with known structures have their N-termini truncated. By contrast, the Rhodopila globiformis RC contains a full-length tetra-heme Cyt with its N-terminus embedded in the membrane forming an α-helix as the membrane anchor. Comparison of the N-terminal regions of the Cyt with PufX polypeptides widely distributed in Rhodobacter species reveals significant structural similarities, supporting a longstanding hypothesis that PufX is phylogenetically related to the N-terminus of the RC-bound Cyt subunit and that a common ancestor of phototrophic Proteobacteria contained a full-length tetra-heme Cyt subunit that evolved independently through partial deletions of its pufC gene. Eleven copies of a novel γ-like polypeptide were also identified in the bacteriochlorophyll a-containing Rhodopila globiformis LH1 complex; γ-polypeptides have previously been found only in the LH1 of bacteriochlorophyll b-containing species. These features are discussed in relation to their predicted functions of stabilizing the LH1 structure and regulating quinone transport under the warm acidic conditions.
#1: Journal: Commun Biol / Year: 2022
Title: An LH1-RC photocomplex from an extremophilic phototroph provides insight into origins of two photosynthesis proteins
Authors: Tani, K. / Kanno, R. / Kurosawa, K. / Takaichi, S. / Nagashima, K.V.P. / Hall, M. / Yu, L.-J. / Kimura, Y. / Madigan, M.T. / Mizoguchi, A. / Humbel, B.M. / Wang-Otomo, Z.-Y.
History
DepositionMay 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Photosynthetic reaction center cytochrome c subunit
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Photosynthetic reaction center H subunit
A: Light-harvesting protein
B: Light-harvesting protein
D: Light-harvesting protein
E: Light-harvesting protein
F: Light-harvesting protein
G: Light-harvesting protein
I: Light-harvesting protein
J: Light-harvesting protein
K: Light-harvesting protein
N: Light-harvesting protein
O: Light-harvesting protein
P: Light-harvesting protein
Q: Light-harvesting protein
R: Light-harvesting protein
S: Light-harvesting protein
T: Light-harvesting protein
U: Light-harvesting protein
V: Light-harvesting protein
W: Light-harvesting protein
X: Light-harvesting protein
Y: Light-harvesting protein
Z: Light-harvesting protein
1: Light-harvesting protein
2: Light-harvesting protein
3: Light-harvesting protein
4: Light-harvesting protein
5: Light-harvesting protein
6: Light-harvesting protein
7: Light-harvesting protein
8: Light-harvesting protein
9: Light-harvesting protein
0: Light-harvesting protein
a: Light-harvesting protein LH1 Gamma-like
b: Light-harvesting protein LH1 Gamma-like
c: Light-harvesting protein LH1 Gamma-like
d: Light-harvesting protein LH1 Gamma-like
e: Light-harvesting protein LH1 Gamma-like
f: Light-harvesting protein LH1 Gamma-like
g: Light-harvesting protein LH1 Gamma-like
h: Light-harvesting protein LH1 Gamma-like
i: Light-harvesting protein LH1 Gamma-like
j: Light-harvesting protein LH1 Gamma-like
k: Light-harvesting protein LH1 Gamma-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)481,882145
Polymers400,14547
Non-polymers81,73698
Water9,692538
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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Photosynthetic reaction center ... , 2 types, 2 molecules CH

#1: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 37945.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodopila globiformis (bacteria) / References: UniProt: A0A2S6NEK5
#4: Protein Photosynthetic reaction center H subunit


Mass: 28383.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodopila globiformis (bacteria) / References: UniProt: A0A2S6MZS1

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

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


Mass: 30697.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodopila globiformis (bacteria) / References: UniProt: A0A2S6NEG7
#3: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 36345.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodopila globiformis (bacteria) / References: UniProt: A0A2S6NEP5

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Light-harvesting ... , 3 types, 43 molecules ADFIKOQSUWY13579BEGJNPRTVXZ246...

#5: Protein
Light-harvesting protein


Mass: 7048.523 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Rhodopila globiformis (bacteria) / References: UniProt: A0A2S6NEK3
#6: Protein
Light-harvesting protein


Mass: 7877.075 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Rhodopila globiformis (bacteria) / References: UniProt: A0A2S6NEL9
#7: Protein/peptide
Light-harvesting protein LH1 Gamma-like


Mass: 2542.199 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Rhodopila globiformis (bacteria)

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Sugars , 1 types, 5 molecules

#13: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 11 types, 631 molecules

#8: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#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 / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#10: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A / Pheophytin


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


Mass: 863.343 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C59H90O4
#14: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#15: Chemical ChemComp-MQ9 / MENAQUINONE-9 / Vitamin K2


Mass: 785.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H80O2
#16: Chemical
ChemComp-I7D / (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E},28~{E})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26,28-dodecaen-5-one / R.g.Keto-II


Mass: 612.924 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C42H60O3 / Feature type: SUBJECT OF INVESTIGATION
#17: 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.: 9 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#18: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 744.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#19: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O

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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 LH1-RC complex from the purple phototrophic bacterium Rhodopila globiformis
Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightValue: 0.4 MDa / Experimental value: NO
Source (natural)Organism: Rhodopila globiformis (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
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 FIELDBright-field microscopy / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 38.9 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20_4459: / 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
3D reconstructionResolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128119 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 40 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 5Y5S

5y5s

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00630386
ELECTRON MICROSCOPYf_angle_d2.57141735
ELECTRON MICROSCOPYf_dihedral_angle_d14.60311949
ELECTRON MICROSCOPYf_chiral_restr0.0484290
ELECTRON MICROSCOPYf_plane_restr0.0044854

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