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- PDB-8z83: Photosynthetic LH1-RC complex from the purple bacterium Halorhodo... -

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Entry
Database: PDB / ID: 8z83
TitlePhotosynthetic LH1-RC complex from the purple bacterium Halorhodospira halophila
Components
  • (Antenna complex, alpha/beta ...) x 4
  • (Photosynthetic reaction center ...) x 2
  • (Reaction center protein ...) x 2
KeywordsPHOTOSYNTHESIS / LH1-RC
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 / endomembrane system / metal ion binding / membrane / 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, M subunit / Photosynthetic reaction centre, L subunit / : / 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 / SPIRILLOXANTHIN / : / HEME C / MENAQUINONE 8 / Chem-PGV / PALMITIC ACID / Ubiquinone-8 ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / SPIRILLOXANTHIN / : / HEME C / MENAQUINONE 8 / Chem-PGV / PALMITIC ACID / Ubiquinone-8 / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / Reaction center protein L chain / Reaction center protein M chain / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsTani, K. / Kanno, R. / Nagashima, K.V.P. / Hiwatashi, N. / Kawakami, M. / Nakata, K. / Nagashima, S. / Inoue, K. / Takaichi, S. / Purba, E.R. ...Tani, K. / Kanno, R. / Nagashima, K.V.P. / Hiwatashi, N. / Kawakami, M. / Nakata, K. / Nagashima, S. / Inoue, K. / Takaichi, S. / Purba, E.R. / Hall, M. / Yu, L.-J. / Madigan, M.T. / Mizoguchi, A. / Humbel, B.M. / Kimura, Y. / 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: Commun Biol / Year: 2025
Title: A Native LH1-RC-HiPIP Supercomplex from an Extremophilic Phototroph.
Authors: Kazutoshi Tani / Ryo Kanno / Kenji V P Nagashima / Mai Kawakami / Naho Hiwatashi / Kazuna Nakata / Sakiko Nagashima / Kazuhito Inoue / Shinichi Takaichi / Endang R Purba / Malgorzata Hall / ...Authors: Kazutoshi Tani / Ryo Kanno / Kenji V P Nagashima / Mai Kawakami / Naho Hiwatashi / Kazuna Nakata / Sakiko Nagashima / Kazuhito Inoue / Shinichi Takaichi / Endang R Purba / Malgorzata Hall / Long-Jiang Yu / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Yukihiro Kimura / Zheng-Yu Wang-Otomo /
Abstract: Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic purple phototrophic bacterium and has been widely used as a model for exploring the osmoadaptive and ...Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic purple phototrophic bacterium and has been widely used as a model for exploring the osmoadaptive and photosynthetic strategies employed by phototrophic extreme halophiles that enable them to thrive in hypersaline environments. Here we present the cryo-EM structures of (1) a unique native Hlr. halophila triple-complex formed from light-harvesting (LH1), the reaction center (RC), and high-potential iron-sulfur protein (HiPIP) at 2.44 Å resolution, and (2) a HiPIP-free LH1-RC complex at 2.64 Å resolution. Differing from the LH1 in the Hlr. halophila LH1-LH2 co-complex where LH1 encircles LH2, the RC-associated LH1 complex consists of 16 (rather than 18) αβ-subunits circularly surrounding the RC. These distinct forms of LH1 indicate that the number of subunits in a Hlr. halophila LH1 complex is flexible and its size is a function of the photocomplex it encircles. Like LH1 in the LH1-LH2 co-complex, the RC-associated LH1 complex also contained two forms of αβ-polypeptides and both dimeric and monomeric molecules of bacteriochlorophyll a. The majority of the isolated Hlr. halophila LH1-RC complexes contained the electron donor HiPIP bound to the surface of the RC cytochrome subunit near the heme-1 group. The bound HiPIP consisted of an N-terminal functional domain and a long C-terminal extension firmly attached to the cytochrome subunit. Despite overall highly negative surface-charge distributions for both the cytochrome subunit and HiPIP, the interface between the two proteins was relatively uncharged and neutral, forming a pathway for electron tunneling. The structure of the Hlr. halophila LH1-RC-HiPIP complex provides insights into the mechanism of light energy acquisition coupled with a long-distance electron donating process toward the charge separation site in a multi-extremophilic phototroph.
History
DepositionApr 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: Antenna complex, alpha/beta subunit
B: Antenna complex, alpha/beta subunit
D: Antenna complex, alpha/beta subunit
E: Antenna complex, alpha/beta subunit
F: Antenna complex, alpha/beta subunit
G: Antenna complex, alpha/beta subunit
I: Antenna complex, alpha/beta subunit
J: Antenna complex, alpha/beta subunit
K: Antenna complex, alpha/beta subunit
N: Antenna complex, alpha/beta subunit
O: Antenna complex, alpha/beta subunit
P: Antenna complex, alpha/beta subunit
Q: Antenna complex, alpha/beta subunit
R: Antenna complex, alpha/beta subunit
S: Antenna complex, alpha/beta subunit
T: Antenna complex, alpha/beta subunit
U: Antenna complex, alpha/beta subunit
V: Antenna complex, alpha/beta subunit
W: Antenna complex, alpha/beta subunit
X: Antenna complex, alpha/beta subunit
Y: Antenna complex, alpha/beta subunit
Z: Antenna complex, alpha/beta subunit
1: Antenna complex, alpha/beta subunit
2: Antenna complex, alpha/beta subunit
3: Antenna complex, alpha/beta subunit
4: Antenna complex, alpha/beta subunit
5: Antenna complex, alpha/beta subunit
6: Antenna complex, alpha/beta subunit
7: Antenna complex, alpha/beta subunit
8: Antenna complex, alpha/beta subunit
9: Antenna complex, alpha/beta subunit
0: Antenna complex, alpha/beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)490,926168
Polymers385,20736
Non-polymers105,719132
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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: 40439.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622
#4: Protein Photosynthetic reaction center H subunit


Mass: 30904.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622

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

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


Mass: 30718.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622 / References: UniProt: A0A2L1K3P0
#3: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 35925.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622 / References: UniProt: A0A2L1K3T5

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Antenna complex, alpha/beta ... , 4 types, 32 molecules AFKQUY37BGNRVZ48DIOSW159EJPTX260

#5: Protein
Antenna complex, alpha/beta subunit


Mass: 7275.500 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622 / References: UniProt: A1WWW5
#6: Protein
Antenna complex, alpha/beta subunit


Mass: 8068.154 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622 / References: UniProt: A1WWW6
#7: Protein
Antenna complex, alpha/beta subunit


Mass: 7664.882 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622 / References: UniProt: A1WXF8
#8: Protein
Antenna complex, alpha/beta subunit


Mass: 7893.913 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622 / References: UniProt: A1WXF9

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Sugars , 1 types, 13 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 13 types, 124 molecules

#9: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-Z41 / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate


Mass: 568.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68O5
#12: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#14: 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.: 42 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#15: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#17: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C49H74O4
#18: 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.: 9 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#19: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#20: Chemical ChemComp-MQ8 / MENAQUINONE 8 / 2-METHYL-3-(3,7,11,15,19,23,27,31-OCTAMETHYL-DOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL)-[1,4]NAPTHOQUINONE


Mass: 717.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H72O2
#21: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C42H60O2
#22: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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

Component
IDNameTypeEntity IDParent-IDSource
1Photosynthetic LH1-RC complex from the purple phototrophic bacterium Halorhodospira halophilaCOMPLEX#1-#5, #7-#8, #60NATURAL
2LH1-RC complex of Halorhodospira halophilaCOMPLEX#1-#5, #7-#8, #61NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Halorhodospira halophila (bacteria)1053BN9622
32Halorhodospira halophila (bacteria)1053BN9622
Buffer solutionpH: 8
SpecimenConc.: 6 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: 90 % / 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 / Nominal defocus max: 2700 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 331335
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44938 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 20 / 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_d0.00629065
ELECTRON MICROSCOPYf_angle_d2.96839862
ELECTRON MICROSCOPYf_dihedral_angle_d18.87911746
ELECTRON MICROSCOPYf_chiral_restr0.1083883
ELECTRON MICROSCOPYf_plane_restr0.0044646

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