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- EMDB-62662: Cryo-EM structure of the LH1 complex from Roseiflexus castenholzii -

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Basic information

Entry
Database: EMDB / ID: EMD-62662
TitleCryo-EM structure of the LH1 complex from Roseiflexus castenholzii
Map data
Sample
  • Complex: LH1 complex
    • Protein or peptide: Beta subunit of light-harvesting 1
    • Protein or peptide: Alpha subunit of light-harvesting 1
  • Ligand: Trans-Geranyl BACTERIOCHLOROPHYLL A
Keywordslight harvesting / Roseiflexus castenholzii / photosynthesis / gene heterologous expression / STRUCTURAL PROTEIN
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, 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
Alpha subunit of light-harvesting 1 / Beta subunit of light-harvesting 1
Similarity search - Component
Biological speciesRoseiflexus castenholzii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsWang L / Yu L-J
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC341800 China
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2026
Title: Assembly, selectivity, and compatibility of bacterial photosynthetic complexes from divergent species detected in a chimeric strain.
Authors: Lu Wang / Yi-Hao Yan / Guang-Lei Wang / Xing-Yu Yue / Chen-Hui Qi / Mei-Juan Zou / Zheng-Yu Wang-Otomo / Michael T Madigan / Yueyong Xin / Long-Jiang Yu /
Abstract: Photosynthetic complexes comprising light-harvesting (LH) and reaction center (RC) components are essential for biological energy conversion in photosynthesis. Assembly of these multi-protein ...Photosynthetic complexes comprising light-harvesting (LH) and reaction center (RC) components are essential for biological energy conversion in photosynthesis. Assembly of these multi-protein structures is a topic of great interest, and assembly mechanisms appear to reflect the evolutionary diversity of the particular phototrophic organism. Here we constructed a photosynthetic chimera expressing the Roseiflexus castenholzii LH and Rhodospirillum rubrum RC complexes in a photocomplex-deficient Rsp. rubrum mutant, and spectroscopy confirmed LH expression with absorption maxima at 878 and 801 nm. The chimeric strain grew slower phototrophically than wildtype but faster than a strain containing only the RC, indicating partial energy transfer from LH to RC. Cryo-EM structural analysis revealed that the Rfl. castenholzii LH independently assembled into a closed ring of 15 αβ heterodimers lacking carotenoids, resulting in a blue-shifted Q transition, while the Rsp. rubrum RC formed a separate complex with an RC:LH ratio of ∼17:1 instead of a typical 1:1. Structural differences, including the absence of two Rfl. castenholzii-specific small proteins, likely precluded formation of a conjoined LH-RC in the chimeric strain. These results reveal that distinct photocomplex assembly strategies exist in phylogenetically divergent species and underscore the modularity and adaptability of photosynthetic complexes, offering insights for artificial photosystem design.
History
DepositionDec 10, 2024-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62662.png

Downloads & links

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Map

FileDownload / File: emd_62662.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 400 pix.
= 323.2 Å		0.81 Å/pix.
x 400 pix.
= 323.2 Å		0.81 Å/pix.
x 400 pix.
= 323.2 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.264
Minimum - Maximum-2.1916192 - 3.0820599
Average (Standard dev.)0.00041234854 (±0.047708124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 323.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62662_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_62662_half_map_2.map
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Sample components

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Entire : LH1 complex

EntireName: LH1 complex
Components
  • Complex: LH1 complex
    • Protein or peptide: Beta subunit of light-harvesting 1
    • Protein or peptide: Alpha subunit of light-harvesting 1
  • Ligand: Trans-Geranyl BACTERIOCHLOROPHYLL A

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Supramolecule #1: LH1 complex

SupramoleculeName: LH1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Roseiflexus castenholzii (bacteria)

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Macromolecule #1: Beta subunit of light-harvesting 1

MacromoleculeName: Beta subunit of light-harvesting 1 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Molecular weightTheoretical: 6.432513 KDa
SequenceString:
MTDKPQNDLV PDQWKPLFNN AEWLVHDIVV KTIYGGLIIA VIAHVLCWAW TPWIR

UniProtKB: Beta subunit of light-harvesting 1

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Macromolecule #2: Alpha subunit of light-harvesting 1

MacromoleculeName: Alpha subunit of light-harvesting 1 / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Molecular weightTheoretical: 4.724656 KDa
SequenceString:
MKDRPFEFRT SVVVSTLLGL VMALLIHFVV LSSGAFNWLR AP

UniProtKB: Alpha subunit of light-harvesting 1

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Macromolecule #3: Trans-Geranyl BACTERIOCHLOROPHYLL A

MacromoleculeName: Trans-Geranyl BACTERIOCHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 45 / Formula: 07D
Molecular weightTheoretical: 901.425 Da
Chemical component information

ChemComp-07D:
Trans-Geranyl BACTERIOCHLOROPHYLL A

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8iug

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207356
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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