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- PDB-7tv3: LH2-LH3 antenna in parallel configuration embedded in a nanodisc -

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Basic information

Entry
Database: PDB / ID: 7tv3
TitleLH2-LH3 antenna in parallel configuration embedded in a nanodisc
Components
  • (Light-harvesting protein B-800/850 ...) x 2
  • (Light-harvesting protein B800-820 ...) x 2
KeywordsPHOTOSYNTHESIS / antenna / membrane protein / nanodisc / bacteriochlorophyll
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
BACTERIOCHLOROPHYLL A / LYCOPENE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.4 Å
AuthorsToporik, H. / Harris, D. / Schlau-Cohen, G.S. / Mazor, Y.
Funding support United States, 5items
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, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light-harvesting protein B-800/850 alpha chain
B: Light-harvesting protein B-800/850 beta 1 chain
C: Light-harvesting protein B-800/850 alpha chain
D: Light-harvesting protein B-800/850 alpha chain
E: Light-harvesting protein B-800/850 beta 1 chain
F: Light-harvesting protein B-800/850 beta 1 chain
G: Light-harvesting protein B-800/850 alpha chain
H: Light-harvesting protein B-800/850 beta 1 chain
I: Light-harvesting protein B-800/850 alpha chain
J: Light-harvesting protein B-800/850 beta 1 chain
K: Light-harvesting protein B-800/850 alpha chain
L: Light-harvesting protein B-800/850 beta 1 chain
M: Light-harvesting protein B-800/850 alpha chain
N: Light-harvesting protein B-800/850 beta 1 chain
O: Light-harvesting protein B-800/850 alpha chain
P: Light-harvesting protein B-800/850 beta 1 chain
Q: Light-harvesting protein B800-820 alpha chain
R: Light-harvesting protein B800-820 beta chain
S: Light-harvesting protein B800-820 alpha chain
T: Light-harvesting protein B800-820 beta chain
U: Light-harvesting protein B800-820 alpha chain
V: Light-harvesting protein B800-820 beta chain
W: Light-harvesting protein B800-820 alpha chain
X: Light-harvesting protein B800-820 beta chain
Y: Light-harvesting protein B800-820 alpha chain
Z: Light-harvesting protein B800-820 beta chain
a: Light-harvesting protein B800-820 alpha chain
b: Light-harvesting protein B800-820 beta chain
c: Light-harvesting protein B800-820 alpha chain
d: Light-harvesting protein B800-820 beta chain
e: Light-harvesting protein B800-820 alpha chain
f: Light-harvesting protein B800-820 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,08896
Polymers179,74632
Non-polymers52,34264
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Light-harvesting protein B-800/850 ... , 2 types, 16 molecules ACDGIKMOBEFHJLNP

#1: Protein
Light-harvesting protein B-800/850 alpha chain / Antenna pigment protein alpha chain


Mass: 6076.175 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Magnetospirillum molischianum (magnetotactic)
References: UniProt: P97253
#2: Protein/peptide
Light-harvesting protein B-800/850 beta 1 chain / Antenna pigment protein beta 1 chain


Mass: 4920.682 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Magnetospirillum molischianum (magnetotactic)
References: UniProt: P95673

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Light-harvesting protein B800-820 ... , 2 types, 16 molecules QSUWYaceRTVXZbdf

#3: Protein
Light-harvesting protein B800-820 alpha chain


Mass: 6219.315 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Magnetospirillum molischianum (magnetotactic)
References: UniProt: Q7M119
#4: Protein/peptide
Light-harvesting protein B800-820 beta chain


Mass: 5252.069 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Magnetospirillum molischianum (magnetotactic)
References: UniProt: Q7M158

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Non-polymers , 2 types, 64 molecules

#5: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-LYC / LYCOPENE


Mass: 536.873 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: LH2 and LH3 antennae / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Magnetospirillum molischianum (magnetotactic)
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54.56 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 11.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22864 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 1LGH

1lgh


Accession code: 1LGH / Source name: PDB / Type: experimental model

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