8YPD

Cryo-EM structure of the LH1 complex from Allochromatium tepidum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Probing the Dual Role of Ca 2+ in the Allochromatium tepidum LH1-RC Complex by Constructing and Analyzing Ca 2+ -Bound and Ca 2+ -Free LH1 Complexes.

Zou, M.J.Sun, S.Wang, G.L.Yan, Y.H.Ji, W.Wang-Otomo, Z.Y.Madigan, M.T.Yu, L.J.

(2025) Biomolecules 15

  • DOI: https://doi.org/10.3390/biom15010124
  • Primary Citation of Related Structures:  
    8YPB, 8YPD

  • PubMed Abstract: 

    The genome of the mildly thermophilic hot spring purple sulfur bacterium, Allochromatium ( Alc .) tepidum , contains a multigene pufBA family that encodes a series of α- and β-polypeptides, collectively forming a heterogeneous light-harvesting 1 (LH1) complex. The Alc. tepidum LH1, therefore, offers a unique model for studying an intermediate phenotype between phototrophic thermophilic and mesophilic bacteria, particularly regarding their LH1 Qy transition and moderately enhanced thermal stability. Of the 16 α-polypeptides in the Alc. tepidum LH1, six α1 bind Ca 2+ to connect with β1- or β3-polypeptides in specific Ca 2+ -binding sites. Here, we use the purple bacterium Rhodospirillum rubrum strain H2 as a host to express Ca 2+ -bound and Ca 2+ -free Alc. tepidum LH1-only complexes composed of α- and β-polypeptides that either contain or lack the calcium-binding motif WxxDxI; purified preparations of each complex were then used to test how Ca 2+ affects their thermostability and spectral features. The cryo-EM structures of both complexes were closed circular rings consisting of 14 αβ-polypeptides. The Q y absorption maximum of Ca 2+ -bound LH1 (α1/β1 and α1/β3) was at 894 nm, while that of Ca 2+ -free (α2/β1) was at 888 nm, indicating that Ca 2+ imparts a Q y transition of 6 nm. Crucially for the ecological success of Alc. tepidum , Ca 2+ -bound LH1 complexes were more thermostable than Ca 2+ -free complexes, indicating that calcium plays at least two major roles in photosynthesis by Alc. tepidum -improving photocomplex stability and modifying its spectrum.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta subunit of light-harvesting 1 complex46Allochromatium tepidumMutation(s): 0 
Gene Names: pufB
Membrane Entity: Yes 
UniProt
Find proteins for O82943 (Allochromatium vinosum)
Explore O82943 
Go to UniProtKB:  O82943
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO82943
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 subunit44Allochromatium tepidumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

Download Ideal Coordinates CCD File 
AB [auth P]
BB [auth Q]
CA [auth b]
DA [auth F]
DB [auth R]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
CRT (Subject of Investigation/LOI)
Query on CRT

Download Ideal Coordinates CCD File 
CB [auth Q]
FA [auth A]
FB [auth S]
HA [auth B]
IB [auth U]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 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)China2022YFC3401800

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release