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- EMDB-36154: Cryo-EM structure of the LH1 complex from thermochromatium tepidum -

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Basic information

Entry
Database: EMDB / ID: EMD-36154
TitleCryo-EM structure of the LH1 complex from thermochromatium tepidum
Map data
Sample
  • Complex: LH1 COMPLEX
    • Protein or peptide: LH1 alpha polypeptide
    • Protein or peptide: LH1 beta polypeptide
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: CALCIUM ION
  • Ligand: SPIRILLOXANTHIN
  • Ligand: DODECANE
KeywordsLH1 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, 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
LH1 beta polypeptide / LH1 alpha polypeptide
Similarity search - Component
Biological speciesThermochromatium tepidum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsWang G-L / Yan Y-H / Yu L-J
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0909600 China
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2024
Title: Molecular structure and characterization of the Thermochromatium tepidum light-harvesting 1 photocomplex produced in a foreign host.
Authors: Yi-Hao Yan / Guang-Lei Wang / Xing-Yu Yue / Fei Ma / Michael T Madigan / Zheng-Yu Wang-Otomo / Mei-Juan Zou / Long-Jiang Yu /
Abstract: Purple phototrophic bacteria possess light-harvesting 1 and reaction center (LH1-RC) core complexes that play a key role in converting solar energy to chemical energy. High-resolution structures of ...Purple phototrophic bacteria possess light-harvesting 1 and reaction center (LH1-RC) core complexes that play a key role in converting solar energy to chemical energy. High-resolution structures of LH1-RC and RC complexes have been intensively studied and have yielded critical insight into the architecture and interactions of their proteins, pigments, and cofactors. Nevertheless, a detailed picture of the structure and assembly of LH1-only complexes is lacking due to the intimate association between LH1 and the RC. To study the intrinsic properties and structure of an LH1-only complex, a genetic system was constructed to express the Thermochromatium (Tch.) tepidum LH1 complex heterologously in a modified Rhodospirillum rubrum mutant strain. The heterologously expressed Tch. tepidum LH1 complex was isolated in a pure form free of the RC and exhibited the characteristic absorption properties of Tch. tepidum. Cryo-EM structures of the LH1-only complexes revealed a closed circular ring consisting of either 14 or 15 αβ-subunits, making it the smallest completely closed LH1 complex discovered thus far. Surprisingly, the Tch. tepidum LH1-only complex displayed even higher thermostability than that of the native LH1-RC complex. These results reveal previously unsuspected plasticity of the LH1 complex, provide new insights into the structure and assembly of the LH1-RC complex, and show how molecular genetics can be exploited to study membrane proteins from phototrophic organisms whose genetic manipulation is not yet possible.
History
DepositionMay 10, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36154.png

Downloads & links

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Map

FileDownload / File: emd_36154.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 360 pix.
= 320.4 Å		0.89 Å/pix.
x 360 pix.
= 320.4 Å		0.89 Å/pix.
x 360 pix.
= 320.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-1.1132876 - 1.6837217
Average (Standard dev.)0.00013778247 (±0.035466667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 320.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36154_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36154_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : LH1 COMPLEX

EntireName: LH1 COMPLEX
Components
  • Complex: LH1 COMPLEX
    • Protein or peptide: LH1 alpha polypeptide
    • Protein or peptide: LH1 beta polypeptide
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: CALCIUM ION
  • Ligand: SPIRILLOXANTHIN
  • Ligand: DODECANE

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Supramolecule #1: LH1 COMPLEX

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

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Macromolecule #1: LH1 alpha polypeptide

MacromoleculeName: LH1 alpha polypeptide / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Thermochromatium tepidum (bacteria)
Molecular weightTheoretical: 7.034442 KDa
SequenceString:
MFTMNANLYK IWLILDPRRV LVSIVAFQIV LGLLIHMIVL STDLNWLDDN IPVSYQALGK K

UniProtKB: LH1 alpha polypeptide

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Macromolecule #2: LH1 beta polypeptide

MacromoleculeName: LH1 beta polypeptide / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Thermochromatium tepidum (bacteria)
Molecular weightTheoretical: 5.534452 KDa
SequenceString:
MAEQKSLTGL TDDEAKEFHA IFMQSMYAWF GLVVIAHLLA WLYRPWL

UniProtKB: LH1 beta polypeptide

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Macromolecule #3: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 28 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 14 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 5 / Number of copies: 14 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

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Macromolecule #6: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 6 / Number of copies: 14 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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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

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5y5s

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47987
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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