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- PDB-8jc9: Cryo-EM structure of the LH1 complex from thermochromatium tepidum -

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Basic information

Entry
Database: PDB / ID: 8jc9
TitleCryo-EM structure of the LH1 complex from thermochromatium tepidum
Components
  • LH1 alpha polypeptide
  • LH1 beta polypeptide
KeywordsPHOTOSYNTHESIS / LH1 COMPLEX
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
BACTERIOCHLOROPHYLL A / SPIRILLOXANTHIN / DODECANE / LH1 beta polypeptide / LH1 alpha polypeptide
Similarity search - Component
Biological speciesThermochromatium tepidum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsWang, G.-L. / Yan, Y.-H. / Yu, L.-J.
Funding support China, 2items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: LH1 alpha polypeptide
2: LH1 beta polypeptide
3: LH1 alpha polypeptide
4: LH1 beta polypeptide
5: LH1 alpha polypeptide
6: LH1 beta polypeptide
7: LH1 alpha polypeptide
8: LH1 beta polypeptide
A: LH1 alpha polypeptide
B: LH1 beta polypeptide
D: LH1 alpha polypeptide
E: LH1 beta polypeptide
F: LH1 alpha polypeptide
G: LH1 beta polypeptide
I: LH1 alpha polypeptide
J: LH1 beta polypeptide
K: LH1 alpha polypeptide
N: LH1 beta polypeptide
O: LH1 alpha polypeptide
P: LH1 beta polypeptide
Q: LH1 alpha polypeptide
R: LH1 beta polypeptide
S: LH1 alpha polypeptide
T: LH1 beta polypeptide
U: LH1 alpha polypeptide
V: LH1 beta polypeptide
Y: LH1 alpha polypeptide
Z: LH1 beta polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,78998
Polymers175,96528
Non-polymers36,82570
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein / Protein/peptide , 2 types, 28 molecules 1357ADFIKOQSUY2468BEGJNPRTVZ

#1: Protein
LH1 alpha polypeptide


Mass: 7034.442 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P2
#2: Protein/peptide
LH1 beta polypeptide


Mass: 5534.452 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P1

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Non-polymers , 4 types, 70 molecules

#3: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C42H60O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C12H26

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Details

Has ligand of interestY
Has protein modificationN

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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: LH1 COMPLEX / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Thermochromatium tepidum (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 63.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47987 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00813901
ELECTRON MICROSCOPYf_angle_d1.89419273
ELECTRON MICROSCOPYf_dihedral_angle_d19.8725453
ELECTRON MICROSCOPYf_chiral_restr0.2281997
ELECTRON MICROSCOPYf_plane_restr0.0052115

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