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- EMDB-28963: LH2-LH3 antenna in parallel configuration embedded in a nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-28963
TitleLH2-LH3 antenna in parallel configuration embedded in a nanodisc
Map dataparallel LHII-LHIII dimer in nanodisk
Sample
  • Complex: LHII-LHIII complex in nanodisk
    • 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: 11.3 Å
AuthorsToporik H / Harris D / Schlau-Cohen GS / Mazor Y
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
Department of Energy (DOE, United States)DE-SC0022956 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
DepositionNov 29, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28963.png

Downloads & links

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Map

FileDownload / File: emd_28963.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationparallel LHII-LHIII dimer in nanodisk
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.75 Å/pix.
x 150 pix.
= 262.5 Å		1.75 Å/pix.
x 150 pix.
= 262.5 Å		1.75 Å/pix.
x 150 pix.
= 262.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0112
Minimum - Maximum-0.010469139 - 0.030414507
Average (Standard dev.)0.0014521091 (±0.003080231)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 262.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28963_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28963_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LHII-LHIII complex in nanodisk

EntireName: LHII-LHIII complex in nanodisk
Components
  • Complex: LHII-LHIII complex in nanodisk
    • 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: LHII-LHIII complex in nanodisk

SupramoleculeName: LHII-LHIII complex in nanodisk / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Magnetospirillum molischianum (magnetotactic)
Molecular weightTheoretical: 200 KDa

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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: 6.08812 KDa
SequenceString:
SNPKDDYKIW LVINPSTWLP VIWIVALLTA IAVHSFVLSV PGYNFLASAA AKTAAK

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: 5.120873 KDa
SequenceString:
AERSLSGLTE EEAVAVHDQF KTTFSAFILL AAVAHVLVWI WKPWF

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: 5.94498 KDa
SequenceString:
SNPKDDYKIW LVINPSTWLP VIWIVATVVA IAVHAAVLAA PGFNWIALGA AKSAAK

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: 5.120873 KDa
SequenceString:
AERSLSGLTE EEAIAVHDQF KTTFSAFIIL AAVAHVLVWV WKPWF

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

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 75.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11133
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8fbb:
LH2-LH3 antenna in parallel configuration embedded in a nanodisc

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