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- EMDB-39835: Photosynthetic LH2-LH1 complex from the purple bacterium Halorhod... -

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Basic information

Entry
Database: EMDB / ID: EMD-39835
TitlePhotosynthetic LH2-LH1 complex from the purple bacterium Halorhodospira halophila
Map datafull map
Sample
  • Complex: Photosynthetic LH2-LH1 complex from the purple phototrophic bacterium Halorhodospira halophila
    • Complex: LH2-LH1 complex of Halorhodospira halophila
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: SPIRILLOXANTHIN
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
KeywordsLH2-LH1 COMPLEX / PHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / : / 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
Similarity search - Domain/homology
Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsTani K / Nagashima KVP / Kanno R / Hiwatashi N / Kawakami M / Nakata K / Nagashima S / Inoue K / Takaichi S / Purba ER ...Tani K / Nagashima KVP / Kanno R / Hiwatashi N / Kawakami M / Nakata K / Nagashima S / Inoue K / Takaichi S / Purba ER / Hall M / Yu L-J / Madigan MT / Mizoguchi A / Humbel BM / Kimura Y / Wang-Otomo Z-Y
Funding support Japan, 6 items
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: 2025
Title: A distinct double-ring LH1-LH2 photocomplex from an extremophilic phototroph.
Authors: Kazutoshi Tani / Kenji V P Nagashima / Risa Kojima / Masaharu Kondo / Ryo Kanno / Issei Satoh / Mai Kawakami / Naho Hiwatashi / Kazuna Nakata / Sakiko Nagashima / Kazuhito Inoue / Yugo Isawa ...Authors: Kazutoshi Tani / Kenji V P Nagashima / Risa Kojima / Masaharu Kondo / Ryo Kanno / Issei Satoh / Mai Kawakami / Naho Hiwatashi / Kazuna Nakata / Sakiko Nagashima / Kazuhito Inoue / Yugo Isawa / Ryoga Morishita / Shinichi Takaichi / Endang R Purba / Malgorzata Hall / Long-Jiang Yu / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Yukihiro Kimura / Yutaka Nagasawa / Takehisa Dewa / Zheng-Yu Wang-Otomo /
Abstract: Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic phototrophic purple sulfur bacterium isolated from a hypersaline lake in the Libyan Desert whose total ...Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic phototrophic purple sulfur bacterium isolated from a hypersaline lake in the Libyan Desert whose total salinity exceeded 35% at pH 10.7. Here we present a cryo-EM structure of the native LH1-LH2 co-complex from strain BN9622 at 2.22 Å resolution. Surprisingly, the LH1-LH2 co-complex consists of a double-ring cylindrical structure with the larger LH1 ring encircling a smaller LH2 ring. The Hlr. halophila LH1 contains 18 αβ-subunits and additional bacteriochlorophyll a (BChl a) molecules that absorb maximally at 797 nm. The LH2 ring is composed of 9 αβ-subunits, and the BChl a molecules in the co-complex form extensive intra- and inter-complex networks to allow near 100% efficiency of energy transfer to its surrounding LH1. The additional LH1-B797 BChls a are located in such a manner that they facilitate exciton transfer from monomeric BChls in LH2 to the dimeric BChls in LH1. The structural features of the strain BN9622 LH1-LH2 co-complex may have evolved to allow a minimal LH2 complex to maximize excitation transfer to the core complex and effectively harvest light in the physiologically demanding ecological niche of this purple bacterium.
History
DepositionApr 21, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39835.png

Downloads & links

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Map

FileDownload / File: emd_39835.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å		0.82 Å/pix.
x 400 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.12252128 - 0.2516624
Average (Standard dev.)0.000012586307 (±0.0077760834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: odd-half map

Fileemd_39835_half_map_1.map
Annotationodd-half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: even-half map

Fileemd_39835_half_map_2.map
Annotationeven-half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Photosynthetic LH2-LH1 complex from the purple phototrophic bacte...

EntireName: Photosynthetic LH2-LH1 complex from the purple phototrophic bacterium Halorhodospira halophila
Components
  • Complex: Photosynthetic LH2-LH1 complex from the purple phototrophic bacterium Halorhodospira halophila
    • Complex: LH2-LH1 complex of Halorhodospira halophila
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
      • Protein or peptide: Antenna complex, alpha/beta subunit
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: SPIRILLOXANTHIN
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE

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Supramolecule #1: Photosynthetic LH2-LH1 complex from the purple phototrophic bacte...

SupramoleculeName: Photosynthetic LH2-LH1 complex from the purple phototrophic bacterium Halorhodospira halophila
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622

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Supramolecule #2: LH2-LH1 complex of Halorhodospira halophila

SupramoleculeName: LH2-LH1 complex of Halorhodospira halophila / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622

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Macromolecule #1: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 7.2755 KDa
SequenceString:
MWRLWKLYDP RRVLIGIFSW LAVLALVIHF ILLSTDRFNW VGGAAVSSVS ESAEEVSALP PRQV

UniProtKB: Antenna complex, alpha/beta subunit

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Macromolecule #2: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 8.068154 KDa
SequenceString:
MADNMSLTGL SDEEAKEFHS IFMQSFLIFT AVAVVAHFLA WAWRPWIPGA EGYGSVIEGV HNVTAAVSQI APLAG

UniProtKB: Antenna complex, alpha/beta subunit

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Macromolecule #3: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 3 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 7.664882 KDa
SequenceString:
MWRMWKILDY RRTVVLAHVG MAVLALLIHF ILLSTENFNW LQGNPYGDAE SAAEVADAAV MPQQREV

UniProtKB: Antenna complex, alpha/beta subunit

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Macromolecule #4: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 4 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 7.893913 KDa
SequenceString:
MADEMRNVSD EEAKEFHAMF SQAFTVYIGV AVVAHILAWA WRPWIPGDEG FGAALIEGAN AVTAAVQSIA PIAA

UniProtKB: Antenna complex, alpha/beta subunit

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Macromolecule #5: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 5 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 7.658842 KDa
SequenceString:
(CXM)NQARIWLVV KPSVGLPLFL GVVLLISLLV HGAILTNTSW YPAFFEGNAA AEIPASEIAE SDALATRESM V

UniProtKB: Antenna complex, alpha/beta subunit

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Macromolecule #6: Antenna complex, alpha/beta subunit

MacromoleculeName: Antenna complex, alpha/beta subunit / type: protein_or_peptide / ID: 6 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Halorhodospira halophila (bacteria) / Strain: BN9622
Molecular weightTheoretical: 6.70149 KDa
SequenceString:
MRDRDDFVDF DDPNRVWPSG LTLPEAEELH SYVLDGARIF FGIAVVAHVL AFAYSPWLG

UniProtKB: Antenna complex, alpha/beta subunit

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Macromolecule #7: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 7 / Number of copies: 72 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #8: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 8 / Number of copies: 45 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #9: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 9 / Number of copies: 18 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

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Macromolecule #10: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 10 / Number of copies: 36 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6.0 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.1 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 331335
Startup modelType of model: OTHER
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 126108
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5y5s

source_name: PDB, initial_model_type: experimental model

1nkz

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 70 / Target criteria: Correlation coefficient
Output model

PDB-8z81:
Photosynthetic LH2-LH1 complex from the purple bacterium Halorhodospira halophila

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