8JC8

Cryo-EM structure of the LH1 complex from thermochromatium tepidum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Molecular structure and characterization of the Thermochromatium tepidum light-harvesting 1 photocomplex produced in a foreign host.

Yan, Y.H.Wang, G.L.Yue, X.Y.Ma, F.Madigan, M.T.Wang-Otomo, Z.Y.Zou, M.J.Yu, L.J.

(2024) Biochim Biophys Acta Bioenerg 1865: 149050-149050

  • DOI: https://doi.org/10.1016/j.bbabio.2024.149050
  • Primary Citation of Related Structures:  
    8JC8, 8JC9

  • PubMed 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 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.


  • Organizational Affiliation

    Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LH1 beta polypeptide47Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P1 (Thermochromatium tepidum)
Explore D2Z0P1 
Go to UniProtKB:  D2Z0P1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2Z0P1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LH1 alpha polypeptide57Thermochromatium tepidumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D2Z0P2 (Thermochromatium tepidum)
Explore D2Z0P2 
Go to UniProtKB:  D2Z0P2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2Z0P2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

Download Ideal Coordinates CCD File 
AC [auth Q]
AD [auth X]
BB [auth D]
CC [auth R]
EA [auth 2]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
CRT (Subject of Investigation/LOI)
Query on CRT

Download Ideal Coordinates CCD File 
AB [auth D]
DB [auth E]
EC [auth S]
IA [auth 3]
JC [auth U]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
8K6
Query on 8K6

Download Ideal Coordinates CCD File 
DC [auth R]
EB [auth E]
FA [auth 2]
IB [auth G]
IC [auth T]
Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
BC [auth Q]
CB [auth D]
GC [auth S]
HA [auth 3]
HB [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFA0909600
Ministry of Science and Technology (MoST, China)China2022YFC3401800

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release