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- PDB-8zk2: Cryo-EM structure of photosynthetic LH1-RC core complex of Roseos... -

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Basic information

Entry
Database: PDB / ID: 8zk2
TitleCryo-EM structure of photosynthetic LH1-RC core complex of Roseospirillum parvum
Components
  • (Photosynthetic reaction center ...) x 2
  • (Reaction center protein ...) x 2
  • Alpha subunit of light-harvesting 1 complex
  • Beta subunit of light-harvesting 1 complex
KeywordsPHOTOSYNTHESIS / LH1-RC core complex / ROSEOSPIRILLUM PARVUM 930I
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosystem II / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / endomembrane system / oxidoreductase activity / electron transfer activity ...organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosystem II / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / endomembrane system / oxidoreductase activity / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 / : / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / Photosynthetic reaction centre, M subunit / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Octadecane / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / HEME C / MENAQUINONE 8 / Chem-PGV / Photosynthetic reaction center H subunit / Photosynthetic reaction center cytochrome c subunit ...Octadecane / BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / HEME C / MENAQUINONE 8 / Chem-PGV / Photosynthetic reaction center H subunit / Photosynthetic reaction center cytochrome c subunit / Reaction center protein M chain / Reaction center protein L chain / 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: 2.65 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

Downloads & links

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Assembly

Deposited unit
C: Photosynthetic reaction center cytochrome c subunit
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Photosynthetic reaction center H subunit
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
O: Beta subunit of light-harvesting 1 complex
P: 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
W: Beta subunit of light-harvesting 1 complex
X: Alpha subunit of light-harvesting 1 complex
Y: Beta subunit of light-harvesting 1 complex
Z: Alpha 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,577147
Polymers368,71836
Non-polymers73,859111
Water00
1


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

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Components

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Photosynthetic reaction center ... , 2 types, 2 molecules CH

#1: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 39726.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseospirillum parvum (bacteria) / References: UniProt: Q6XBJ5
#4: Protein Photosynthetic reaction center H subunit


Mass: 27770.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseospirillum parvum (bacteria) / References: UniProt: A0A1G7WCA0

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Reaction center protein ... , 2 types, 2 molecules LM

#2: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 30656.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseospirillum parvum (bacteria) / References: UniProt: Q6XBJ7
#3: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 35877.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseospirillum parvum (bacteria) / References: UniProt: Q6XBJ6

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Protein , 2 types, 32 molecules BDFIKOQSUWYacegiAEGJNPRTVXZbdfhj

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


Mass: 7382.300 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Roseospirillum parvum (bacteria) / References: UniProt: Q6XBJ9
#6: Protein
Alpha subunit of light-harvesting 1 complex / Light-harvesting complex 1 alpha chain


Mass: 7285.641 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Roseospirillum parvum (bacteria) / References: UniProt: Q6XBJ8

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Sugars , 1 types, 1 molecules

#13: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 9 types, 110 molecules

#7: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#10: Chemical...
ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C18H38
#11: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-MQ8 / MENAQUINONE 8 / 2-METHYL-3-(3,7,11,15,19,23,27,31-OCTAMETHYL-DOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL)-[1,4]NAPTHOQUINONE


Mass: 717.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H72O2 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C42H60O2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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-RC core complex / Type: COMPLEX / Entity ID: #1-#6 / 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: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 281288 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0128089
ELECTRON MICROSCOPYf_angle_d2.02938827
ELECTRON MICROSCOPYf_dihedral_angle_d20.37410782
ELECTRON MICROSCOPYf_chiral_restr0.2233782
ELECTRON MICROSCOPYf_plane_restr0.0174397

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