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- PDB-8ypd: Cryo-EM structure of the LH1 complex from Allochromatium tepidum -

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Basic information

Entry
Database: PDB / ID: 8ypd
TitleCryo-EM structure of the LH1 complex from Allochromatium tepidum
Components
  • Beta subunit of light-harvesting 1 complex
  • LH1 alpha subunit
KeywordsPHOTOSYNTHESIS / LH1 COMPLEX
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
BACTERIOCHLOROPHYLL A / SPIRILLOXANTHIN / Beta subunit of light-harvesting 1 complex
Similarity search - Component
Biological speciesAllochromatium tepidum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsWang, G.-L. / Sun, S. / Yu, L.-J.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
b: Beta subunit of light-harvesting 1 complex
F: LH1 alpha subunit
A: Beta subunit of light-harvesting 1 complex
B: LH1 alpha subunit
C: Beta subunit of light-harvesting 1 complex
D: LH1 alpha subunit
E: Beta subunit of light-harvesting 1 complex
G: LH1 alpha subunit
H: Beta subunit of light-harvesting 1 complex
I: LH1 alpha subunit
J: Beta subunit of light-harvesting 1 complex
K: LH1 alpha subunit
L: Beta subunit of light-harvesting 1 complex
M: LH1 alpha subunit
N: Beta subunit of light-harvesting 1 complex
O: LH1 alpha subunit
P: Beta subunit of light-harvesting 1 complex
Q: LH1 alpha subunit
R: Beta subunit of light-harvesting 1 complex
S: LH1 alpha subunit
T: Beta subunit of light-harvesting 1 complex
U: LH1 alpha subunit
V: Beta subunit of light-harvesting 1 complex
W: LH1 alpha subunit
X: Beta subunit of light-harvesting 1 complex
Y: LH1 alpha subunit
Z: Beta subunit of light-harvesting 1 complex
a: LH1 alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,16070
Polymers145,28128
Non-polymers33,87942
Water00
1


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

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Components

#1: Protein/peptide
Beta subunit of light-harvesting 1 complex


Mass: 5269.103 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium tepidum (bacteria) / Gene: pufB
Production host: Rhodospirillum rubrum ATCC 11170 (bacteria)
References: UniProt: O82943
#2: Protein/peptide
LH1 alpha subunit


Mass: 5108.121 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium tepidum (bacteria)
Production host: Rhodospirillum rubrum ATCC 11170 (bacteria)
#3: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C42H60O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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 COMPLEX / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Source (recombinant)Organism: Rhodospirillum rubrum ATCC 11170 (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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 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: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 199061 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00512852
ELECTRON MICROSCOPYf_angle_d1.08117822
ELECTRON MICROSCOPYf_dihedral_angle_d18.8532772
ELECTRON MICROSCOPYf_chiral_restr0.0441750
ELECTRON MICROSCOPYf_plane_restr0.0051960

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