RCSB PDB - 8ZK2: Cryo-EM structure of photosynthetic LH1-RC core complex of Roseospirillum parvum

 8ZK2

Cryo-EM structure of photosynthetic LH1-RC core complex of Roseospirillum parvum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Insights into the divergence of the photosynthetic LH1 complex obtained from structural analysis of the unusual photocomplexes of Roseospirillum parvum.

Wang, X.P.Wang, G.L.Fu, Y.Minamino, A.Zou, M.J.Ma, F.Xu, B.Wang-Otomo, Z.Y.Kimura, Y.Madigan, M.T.Overmann, J.Yu, L.J.

(2024) Commun Biol 7: 1658-1658

  • DOI: https://doi.org/10.1038/s42003-024-07354-4
  • Primary Citation of Related Structures:  
    8ZJW, 8ZK2

  • PubMed Abstract: 

    Purple phototrophic bacteria produce two kinds of light-harvesting complexes that function to capture and transmit solar energy: the core antenna (LH1) and the peripheral antenna (LH2). The apoproteins of these antennas, encoded respectively by the genes pufBA and pucBA within and outside the photosynthetic gene cluster, respectively, exhibit conserved amino acid sequences and structural topologies suggesting they were derived from a shared ancestor. Here we present the structures of two photosynthetic complexes from Roseospirillum (Rss.) parvum 930I: an LH1-RC complex and a variant of the LH1 complex also encoded by pufBA that we designate as LH1'. The LH1-RC complex forms a closed elliptical structure consisting of 16 pairs of αβ-polypeptides that surrounds the RC. By contrast, the LH1' complex is a closed ring structure composed of 14 pairs of αβ-polypeptides, and it shows significant similarities to LH2 complexes both spectrally and structurally. Although LH2-like, the LH1' complex is larger than any known LH2 complexes, and genomic analyses of Rss. parvum revealed the absence of pucBA, genes that encode classical LH2 complexes. Characterization of the unique Rss. parvum photocomplexes not only underscores the diversity of such structures but also sheds new light on the evolution of light-harvesting complexes from phototrophic bacteria.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]362Roseospirillum parvumMutation(s): 0 
UniProt
Find proteins for Q6XBJ5 (Roseospirillum parvum)
Explore Q6XBJ5 
Go to UniProtKB:  Q6XBJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XBJ5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]275Roseospirillum parvumMutation(s): 0 
UniProt
Find proteins for Q6XBJ7 (Roseospirillum parvum)
Explore Q6XBJ7 
Go to UniProtKB:  Q6XBJ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XBJ7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]323Roseospirillum parvumMutation(s): 0 
UniProt
Find proteins for Q6XBJ6 (Roseospirillum parvum)
Explore Q6XBJ6 
Go to UniProtKB:  Q6XBJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XBJ6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center H subunitD [auth H]254Roseospirillum parvumMutation(s): 0 
UniProt
Find proteins for A0A1G7WCA0 (Roseospirillum parvum)
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Entity Groups  
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UniProt GroupA0A1G7WCA0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Beta subunit of light-harvesting 1 complex68Roseospirillum parvumMutation(s): 0 
UniProt
Find proteins for Q6XBJ9 (Roseospirillum parvum)
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Go to UniProtKB:  Q6XBJ9
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UniProt GroupQ6XBJ9
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha subunit of light-harvesting 1 complex67Roseospirillum parvumMutation(s): 0 
UniProt
Find proteins for Q6XBJ8 (Roseospirillum parvum)
Explore Q6XBJ8 
Go to UniProtKB:  Q6XBJ8
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UniProt GroupQ6XBJ8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

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AC [auth E]
AE [auth d]
BD [auth S]
CC [auth F]
CD [auth T]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH (Subject of Investigation/LOI)
Query on BPH

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GB [auth M],
VA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
PGV
Query on PGV

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AD [auth R]
CB [auth L]
JB [auth M]
KB [auth M]
MB [auth H]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
MQ8 (Subject of Investigation/LOI)
Query on MQ8

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HB [auth M]MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
CRT (Subject of Investigation/LOI)
Query on CRT

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BC [auth E]
DE [auth e]
FD [auth U]
GC [auth I]
IB [auth M]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
LMT
Query on LMT

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AB [auth L]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
8K6
Query on 8K6

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BB [auth L]
BE [auth d]
GE [auth f]
ID [auth V]
JC [auth J]
Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

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DB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG
Query on MG

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OA [auth C],
PA [auth C],
QA [auth C],
SB [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

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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: 2025-01-22
    Type: Initial release