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- EMDB-26134: LH2-LH3 antenna in anti parallel configuration embedded in a nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-26134
TitleLH2-LH3 antenna in anti parallel configuration embedded in a nanodisc
Map dataLH2-LH3 antenna in anti parallel orientation with nanodisc
Sample
  • Complex: LH2 and LH3 antennae
    • Protein or peptide: Light-harvesting protein B800-820 alpha chain
    • Protein or peptide: Light-harvesting protein B800-820 beta chain
    • Protein or peptide: Light-harvesting protein B-800/850 alpha chain
    • Protein or peptide: Light-harvesting protein B-800/850 beta 1 chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: LYCOPENE
Keywordsantenna / membrane protein / nanodisc / bacteriochlorophyll / PHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / metal ion binding / plasma membrane
Similarity search - Function
Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / 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
Light-harvesting protein B-800/850 beta 1 chain / Light-harvesting protein B-800/850 alpha chain / Light-harvesting protein B800-820 alpha chain / Light-harvesting protein B800-820 beta chain
Similarity search - Component
Biological speciesMagnetospirillum molischianum (magnetotactic)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsToporik H / Harris D
Funding support United States, 5 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0018097 United States
National Science Foundation (NSF, United States)CHE 1800301 United States
National Science Foundation (NSF, United States)CHE 1836913 United States
National Science Foundation (NSF, United States) United States
National Science Foundation (NSF, United States)2034021 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria.
Authors: Dihao Wang / Olivia C Fiebig / Dvir Harris / Hila Toporik / Yi Ji / Chern Chuang / Muath Nairat / Ashley L Tong / John I Ogren / Stephanie M Hart / Jianshu Cao / James N Sturgis / Yuval ...Authors: Dihao Wang / Olivia C Fiebig / Dvir Harris / Hila Toporik / Yi Ji / Chern Chuang / Muath Nairat / Ashley L Tong / John I Ogren / Stephanie M Hart / Jianshu Cao / James N Sturgis / Yuval Mazor / Gabriela S Schlau-Cohen /
Abstract: In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical ...In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical reactions. While the energy transfer dynamics within individual antenna proteins have been extensively studied over the past decades, the dynamics between the proteins are poorly understood due to the heterogeneous organization of the network. Previously reported timescales averaged over such heterogeneity, obscuring individual interprotein energy transfer steps. Here, we isolated and interrogated interprotein energy transfer by embedding two variants of the primary antenna protein from purple bacteria, light-harvesting complex 2 (LH2), together into a near-native membrane disc, known as a nanodisc. We integrated ultrafast transient absorption spectroscopy, quantum dynamics simulations, and cryogenic electron microscopy to determine interprotein energy transfer timescales. By varying the diameter of the nanodiscs, we replicated a range of distances between the proteins. The closest distance possible between neighboring LH2, which is the most common in native membranes, is 25 Å and resulted in a timescale of 5.7 ps. Larger distances of 28 to 31 Å resulted in timescales of 10 to 14 ps. Corresponding simulations showed that the fast energy transfer steps between closely spaced LH2 increase transport distances by ∼15%. Overall, our results introduce a framework for well-controlled studies of interprotein energy transfer dynamics and suggest that protein pairs serve as the primary pathway for the efficient transport of solar energy.
History
DepositionFeb 3, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26134.png

Downloads & links

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Map

FileDownload / File: emd_26134.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLH2-LH3 antenna in anti parallel orientation with nanodisc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.6 Å/pix.
x 200 pix.
= 320. Å		1.6 Å/pix.
x 200 pix.
= 320. Å		1.6 Å/pix.
x 200 pix.
= 320. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.097239174 - 0.13585736
Average (Standard dev.)-0.00003581808 (±0.0049895593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 320.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : LH2 and LH3 antennae

EntireName: LH2 and LH3 antennae
Components
  • Complex: LH2 and LH3 antennae
    • Protein or peptide: Light-harvesting protein B800-820 alpha chain
    • Protein or peptide: Light-harvesting protein B800-820 beta chain
    • Protein or peptide: Light-harvesting protein B-800/850 alpha chain
    • Protein or peptide: Light-harvesting protein B-800/850 beta 1 chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: LYCOPENE

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Supramolecule #1: LH2 and LH3 antennae

SupramoleculeName: LH2 and LH3 antennae / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Magnetospirillum molischianum (magnetotactic)

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Macromolecule #1: Light-harvesting protein B800-820 alpha chain

MacromoleculeName: Light-harvesting protein B800-820 alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Magnetospirillum molischianum (magnetotactic)
Molecular weightTheoretical: 6.219315 KDa
SequenceString:
MSNPKDDYKI WLVINPSTWL PVIWIVALLT AIAVHSFVLS VPGYNFLASA AAKTAAK

UniProtKB: Light-harvesting protein B800-820 alpha chain

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Macromolecule #2: Light-harvesting protein B800-820 beta chain

MacromoleculeName: Light-harvesting protein B800-820 beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Magnetospirillum molischianum (magnetotactic)
Molecular weightTheoretical: 5.252069 KDa
SequenceString:
MAERSLSGLT EEEAVAVHDQ FKTTFSAFIL LAAVAHVLVW IWKPWF

UniProtKB: Light-harvesting protein B800-820 beta chain

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Macromolecule #3: Light-harvesting protein B-800/850 alpha chain

MacromoleculeName: Light-harvesting protein B-800/850 alpha chain / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Magnetospirillum molischianum (magnetotactic)
Molecular weightTheoretical: 6.076175 KDa
SequenceString:
MSNPKDDYKI WLVINPSTWL PVIWIVATVV AIAVHAAVLA APGFNWIALG AAKSAAK

UniProtKB: Light-harvesting protein B-800/850 alpha chain

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Macromolecule #4: Light-harvesting protein B-800/850 beta 1 chain

MacromoleculeName: Light-harvesting protein B-800/850 beta 1 chain / type: protein_or_peptide / ID: 4 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Magnetospirillum molischianum (magnetotactic)
Molecular weightTheoretical: 5.252069 KDa
SequenceString:
MAERSLSGLT EEEAIAVHDQ FKTTFSAFII LAAVAHVLVW VWKPWF

UniProtKB: Light-harvesting protein B-800/850 beta 1 chain

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Macromolecule #5: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 5 / Number of copies: 48 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #6: LYCOPENE

MacromoleculeName: LYCOPENE / type: ligand / ID: 6 / Number of copies: 16 / Formula: LYC
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-LYC:
LYCOPENE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 54.56 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1lgh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71566
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1lgh


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-7tuw:
LH2-LH3 antenna in anti parallel configuration embedded in a nanodisc

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