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- EMDB-39475: Cryo-EM structure of the LH1 complex from Allochromatium tepidum -

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Basic information

Entry
Database: EMDB / ID: EMD-39475
TitleCryo-EM structure of the LH1 complex from Allochromatium tepidum
Map data
Sample
  • Complex: LH1 COMPLEX
    • Protein or peptide: Beta subunit of light-harvesting 1 complex
    • Protein or peptide: LH1 alpha polypeptide
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: CALCIUM ION
  • Ligand: SPIRILLOXANTHIN
KeywordsLH1 COMPLEX / PHOTOSYNTHESIS
Function / homology
Function and homology information


plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / metal ion binding / plasma membrane
Similarity search - Function
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
Beta subunit of light-harvesting 1 complex
Similarity search - Component
Biological speciesAllochromatium tepidum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsWang G-L / Sun S / Yu L-J
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
CitationJournal: Biomolecules / Year: 2025
Title: Probing the Dual Role of Ca in the LH1-RC Complex by Constructing and Analyzing Ca-Bound and Ca-Free LH1 Complexes.
Authors: Mei-Juan Zou / Shuai Sun / Guang-Lei Wang / Yi-Hao Yan / Wei Ji / Zheng-Yu Wang-Otomo / Michael T Madigan / Long-Jiang Yu /
Abstract: The genome of the mildly thermophilic hot spring purple sulfur bacterium, (.) , contains a multigene family that encodes a series of α- and β-polypeptides, collectively forming a heterogeneous ...The genome of the mildly thermophilic hot spring purple sulfur bacterium, (.) , contains a multigene family that encodes a series of α- and β-polypeptides, collectively forming a heterogeneous light-harvesting 1 (LH1) complex. The LH1, therefore, offers a unique model for studying an intermediate phenotype between phototrophic thermophilic and mesophilic bacteria, particularly regarding their LH1 transition and moderately enhanced thermal stability. Of the 16 α-polypeptides in the LH1, six α1 bind Ca to connect with β1- or β3-polypeptides in specific Ca-binding sites. Here, we use the purple bacterium strain H2 as a host to express Ca-bound and Ca-free LH1-only complexes composed of α- and β-polypeptides that either contain or lack the calcium-binding motif WxxDxI; purified preparations of each complex were then used to test how Ca affects their thermostability and spectral features. The cryo-EM structures of both complexes were closed circular rings consisting of 14 αβ-polypeptides. The absorption maximum of Ca-bound LH1 (α1/β1 and α1/β3) was at 894 nm, while that of Ca-free (α2/β1) was at 888 nm, indicating that Ca imparts a transition of 6 nm. Crucially for the ecological success of , Ca-bound LH1 complexes were more thermostable than Ca-free complexes, indicating that calcium plays at least two major roles in photosynthesis by -improving photocomplex stability and modifying its spectrum.
History
DepositionMar 16, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39475.png

Downloads & links

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Map

FileDownload / File: emd_39475.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 360 pix.
= 374.4 Å		1.04 Å/pix.
x 360 pix.
= 374.4 Å		1.04 Å/pix.
x 360 pix.
= 374.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.73579 - 5.6037474
Average (Standard dev.)0.00043987948 (±0.0744166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39475_half_map_1.map
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Half map: #1

Fileemd_39475_half_map_2.map
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Sample components

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Entire : LH1 COMPLEX

EntireName: LH1 COMPLEX
Components
  • Complex: LH1 COMPLEX
    • Protein or peptide: Beta subunit of light-harvesting 1 complex
    • Protein or peptide: LH1 alpha polypeptide
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: CALCIUM ION
  • Ligand: SPIRILLOXANTHIN

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Supramolecule #1: LH1 COMPLEX

SupramoleculeName: LH1 COMPLEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Allochromatium tepidum (bacteria)

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Macromolecule #1: Beta subunit of light-harvesting 1 complex

MacromoleculeName: Beta subunit of light-harvesting 1 complex / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Molecular weightTheoretical: 5.269103 KDa
Recombinant expressionOrganism: Rhodospirillum rubrum ATCC 11170 (bacteria)
SequenceString:
MANSSMTGLT EQEAQEFHGI FVQSMTAFFG IVVIAHILAW LWRPWL

UniProtKB: Beta subunit of light-harvesting 1 complex

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Macromolecule #2: LH1 alpha polypeptide

MacromoleculeName: LH1 alpha polypeptide / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Molecular weightTheoretical: 7.302729 KDa
Recombinant expressionOrganism: Rhodospirillum rubrum ATCC 11170 (bacteria)
SequenceString:
MSPDLWKIWL LIDPRRVLIA VFAFLTILGL AIHMILLSTT EFNWLEDGIP AAKVQQVTPV VPQR

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Macromolecule #3: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 28 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 14 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: SPIRILLOXANTHIN

MacromoleculeName: SPIRILLOXANTHIN / type: ligand / ID: 5 / Number of copies: 14 / Formula: CRT
Molecular weightTheoretical: 596.925 Da
Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

5y5s

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 234287
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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