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- PDB-8zjw: Cryo-EM structure of photosynthetic LH1' complex of Roseospirillu... -

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Basic information

Entry
Database: PDB / ID: 8zjw
TitleCryo-EM structure of photosynthetic LH1' complex of Roseospirillum parvum
Components
  • Alpha subunit of light-harvesting 1 complex
  • Beta subunit of light-harvesting 1 complex
KeywordsPHOTOSYNTHESIS / LH1 prime complex / ROSEOSPIRILLUM PARVUM 930I
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / : / metal ion binding / plasma membrane
Similarity search - Function
Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / SPIRILLOXANTHIN / Alpha subunit of light-harvesting 1 complex / Beta subunit of light-harvesting 1 complex
Similarity search - Component
Biological speciesRoseospirillum parvum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsWang, G.-L. / Wang, X.-P. / Yu, L.-J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
CitationJournal: Commun Biol / Year: 2024
Title: Insights into the divergence of the photosynthetic LH1 complex obtained from structural analysis of the unusual photocomplexes of Roseospirillum parvum.
Authors: Xiang-Ping Wang / Guang-Lei Wang / Yuan Fu / Akane Minamino / Mei-Juan Zou / Fei Ma / Bo Xu / Zheng-Yu Wang-Otomo / Yukihiro Kimura / Michael T Madigan / Jörg Overmann / Long-Jiang Yu /
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 ...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.
History
DepositionMay 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Beta subunit of light-harvesting 1 complex
A: Alpha subunit of light-harvesting 1 complex
D: Beta subunit of light-harvesting 1 complex
E: Alpha subunit of light-harvesting 1 complex
F: Beta subunit of light-harvesting 1 complex
G: Alpha subunit of light-harvesting 1 complex
I: Beta subunit of light-harvesting 1 complex
J: Alpha subunit of light-harvesting 1 complex
K: Beta subunit of light-harvesting 1 complex
N: Alpha subunit of light-harvesting 1 complex
Q: Beta subunit of light-harvesting 1 complex
R: Alpha subunit of light-harvesting 1 complex
S: Beta subunit of light-harvesting 1 complex
T: Alpha subunit of light-harvesting 1 complex
U: Beta subunit of light-harvesting 1 complex
V: Alpha subunit of light-harvesting 1 complex
Y: Beta subunit of light-harvesting 1 complex
a: Beta subunit of light-harvesting 1 complex
b: Alpha subunit of light-harvesting 1 complex
c: Beta subunit of light-harvesting 1 complex
d: Alpha subunit of light-harvesting 1 complex
e: Beta subunit of light-harvesting 1 complex
f: Alpha subunit of light-harvesting 1 complex
g: Beta subunit of light-harvesting 1 complex
h: Alpha subunit of light-harvesting 1 complex
i: Beta subunit of light-harvesting 1 complex
j: Alpha subunit of light-harvesting 1 complex
C: Alpha subunit of light-harvesting 1 complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,99184
Polymers205,35128
Non-polymers46,64056
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Beta subunit of light-harvesting 1 complex / Light-harvesting complex 1 beta chain


Mass: 7382.300 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Roseospirillum parvum (bacteria) / References: UniProt: Q6XBJ9
#2: Protein
Alpha subunit of light-harvesting 1 complex / Light-harvesting complex 1 alpha chain


Mass: 7285.641 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Roseospirillum parvum (bacteria) / References: UniProt: Q6XBJ8
#3: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C42H60O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: LH1 prime complex / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Roseospirillum parvum (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 61.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 397127 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0115316
ELECTRON MICROSCOPYf_angle_d2.27821433
ELECTRON MICROSCOPYf_dihedral_angle_d21.3025838
ELECTRON MICROSCOPYf_chiral_restr0.2712086
ELECTRON MICROSCOPYf_plane_restr0.0062338

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