8Z4V | pdb_00008z4v

LH2 complex from Ectothiorhodospira haloalkaliphila at near-atomic resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Near-atomic cryo-EM structure of the light-harvesting complex LH2 from the sulfur purple bacterium Ectothiorhodospira haloalkaliphila.

Burtseva, A.D.Baymukhametov, T.N.Bolshakov, M.A.Makhneva, Z.K.Mardanov, A.V.Tsedilin, A.M.Zhang, H.Popov, V.O.Ashikhmin, A.A.Boyko, K.M.

(2025) Structure 33: 311-320.e3

  • DOI: https://doi.org/10.1016/j.str.2024.11.015
  • Primary Citation of Related Structures:  
    8Z4V

  • PubMed Abstract: 

    Bacteria with the simplest system for solar energy absorption and conversion use various types of light-harvesting complexes for these purposes. Light-harvesting complex 2 (LH2), an important component of the bacterial photosynthetic apparatus, has been structurally well characterized among purple non-sulfur bacteria. In contrast, so far only one high-resolution LH2 structure from sulfur bacteria is known. Here, we report the near-atomic resolution cryoelectron microscopy (cryo-EM) structure of the LH2 complex from the purple sulfur bacterium Ectothiorhodospira haloalkaliphila, which allowed us to determine the predominant polypeptide composition of this complex and the identification of the most probable type of its carotenoid. Comparison of our structure with the only known LH2 complex from a sulfur bacterium revealed severe differences in the overall ring-like organization. Expanding the architectural universe of bacterial light-harvesting complexes, our results demonstrate that, as observed for non-sulfur bacteria, the LH2 complexes of sulfur bacteria may also exhibit various types of spatial organization.


  • Organizational Affiliation
    • Bach Institute of Biochemistry, Research Center of Biotechnology Russian Academy of Sciences, Leninsky pr-t, 33, bld. 2, Moscow 119071, Russia; Landau Phystech School of Physics and Research, Moscow Institute of Physics and Technology, Institutsky lane, 9, Dolgoprudny, Moscow region 141700, Russia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B:800-850 subunit beta46Ectothiorhodospira haloalkaliphila ATCC 51935Mutation(s): 0 
UniProt
Find proteins for W8KQR0 (Ectothiorhodospira haloalkaliphila)
Explore W8KQR0 
Go to UniProtKB:  W8KQR0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW8KQR0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-800/850 alpha chain70Ectothiorhodospira haloalkaliphila ATCC 51935Mutation(s): 0 
UniProt
Find proteins for W8KE12 (Ectothiorhodospira haloalkaliphila)
Explore W8KE12 
Go to UniProtKB:  W8KE12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW8KE12
Sequence Annotations
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  • 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 
BA [auth H]
CA [auth J]
DA [auth J]
FA [auth K]
GA [auth M]
BA [auth H],
CA [auth J],
DA [auth J],
FA [auth K],
GA [auth M],
HA [auth M],
JA [auth N],
KA [auth P],
LA [auth P],
NA [auth Q],
OA [auth S],
PA [auth S],
Q [auth A],
R [auth A],
RA [auth T],
SA [auth V],
T [auth C],
TA [auth V],
U [auth D],
V [auth D],
VA [auth W],
X [auth E],
Y [auth G],
Z [auth G]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
A1L0S (Subject of Investigation/LOI)
Query on A1L0S

Download Ideal Coordinates CCD File 
AA [auth G]
EA [auth J]
IA [auth M]
MA [auth P]
QA [auth S]
AA [auth G],
EA [auth J],
IA [auth M],
MA [auth P],
QA [auth S],
S [auth A],
UA [auth V],
W [auth D]
Anhydrorhodovibrin
C41 H58 O
OCDSWQXGIQUZCF-AGVJHCIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1
MODEL REFINEMENTServalcat1.6.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation23-74-00062

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Data collection, Database references