9LT4 | pdb_00009lt4

Cryo-EM structure of light harvesting complex 2 from Ery. sanguineus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 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

Cryo-EM structures of photocomplexes from the free-living aerobic anoxygenic phototrophic bacterium Erythrobacter sanguineus.

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

(2025) Structure 

  • DOI: https://doi.org/10.1016/j.str.2025.10.017
  • Primary Citation of Related Structures:  
    9LT4, 9LTI

  • PubMed Abstract: 

    Aerobic anoxygenic phototrophic bacteria (AAPB) are widely distributed in nature and they are important members of the marine phototrophic community. However, a structural and functional understanding of the AAPB photosynthetic apparatus is still lacking. Here, we present cryo-EM structures of the LH1-RC (core) and LH2 (peripheral) photocomplexes from the model aerobic phototroph Erythrobacter (Ery.) sanguineus. The LH1 αβ-heterodimers bind the carotenoids bacteriorubixanthinal and caloxanthin-pigments that are absent from anaerobic anoxygenic phototrophs-to form a closed ring structure. Ery. sanguineus LH1-RC contains a lipid-anchored polypeptide unrelated to any of the auxiliary proteins identified in the core complexes of purple bacteria so far. The Ery. sanguineus LH2 complex shows unique absorption characteristics, with its Q y transition being blue-shifted to 814 nm. This work provides structural insights into the unusual photosynthetic properties of AAPB and points to new avenues to further explore their biology.


  • Organizational Affiliation
    • Photosynthesis Research Center, State Key Laboratory of Forage Breeding-by-Design and Utilization, 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
Light-harvesting protein B-800/814 alpha chain67Erythrobacter sanguineusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 beta chain51Erythrobacter sanguineusMutation(s): 0 
UniProt
Find proteins for A0A1M7SGD0 (Erythrobacter sanguineus)
Explore A0A1M7SGD0 
Go to UniProtKB:  A0A1M7SGD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1M7SGD0
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 
AA [auth I]
AB [auth b]
BA [auth H]
BB [auth b]
CA [auth H]
AA [auth I],
AB [auth b],
BA [auth H],
BB [auth b],
CA [auth H],
DA [auth G],
EA [auth F],
FA [auth F],
GA [auth E],
HA [auth E],
JA [auth D],
KA [auth C],
LA [auth C],
MA [auth B],
NA [auth h],
PA [auth g],
QA [auth g],
S [auth A],
SA [auth f],
U [auth i],
UA [auth e],
VA [auth d],
W [auth a],
WA [auth d],
X [auth a],
YA [auth c],
Z [auth I]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
A1ELD (Subject of Investigation/LOI)
Query on A1ELD

Download Ideal Coordinates CCD File 
IA [auth D]
OA [auth h]
RA [auth g]
T [auth A]
TA [auth f]
IA [auth D],
OA [auth h],
RA [auth g],
T [auth A],
TA [auth f],
V [auth i],
XA [auth d],
Y [auth a],
ZA [auth c]
(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-2-[(1~{Z},3~{Z},5~{E})-8-methoxy-4,8-dimethyl-nona-1,3,5-trienyl]-6,11,15-trimethyl-17-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]heptadeca-2,4,6,8,10,12,14,16-octaenal
C41 H56 O3
DFOYVSCLGRVGJK-PCDZQMFBSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 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
Ministry of Science and Technology (MoST, China)ChinaZR2019ZD48
Ministry of Science and Technology (MoST, China)China2022SZX12

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release