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- PDB-9w1c: LH2 complex from Ectothiorhodospira haloalkaliphila with inhibite... -

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Basic information

Entry
Database: PDB / ID: 9w1c
TitleLH2 complex from Ectothiorhodospira haloalkaliphila with inhibited carotenoid biosynthesis
Components
  • Light-harvesting protein B-800/850 alpha chain
  • Light-harvesting protein B:800-850 subunit beta
KeywordsPHOTOSYNTHESIS / Light-harvesing / purple sulfur bacteria / cryo-EM
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, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / 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 / Antenna complex alpha/beta subunit domain-containing protein / Light-harvesting protein B:800-850 subunit beta
Similarity search - Component
Biological speciesEctothiorhodospira haloalkaliphila ATCC 51935 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.92 Å
AuthorsBurtseva, A.D. / Baymukhametov, T.N. / Popov, V.O. / Ashikhmin, A.A. / Boyko, K.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-74-00062 Russian Federation
CitationJournal: FEBS Lett / Year: 2025
Title: Structural insights into LH2 complexes formed by a purple sulfur bacterium with inhibited carotenoid biosynthesis.
Authors: Anna D Burtseva / Timur N Baymukhametov / Maxim A Bolshakov / Aleksandr S Starodubov / Huawei Zhang / Vladimir O Popov / Aleksandr A Ashikhmin / Konstantin M Boyko /
Abstract: The LH2 complex is essential for light harvesting in many photosynthetic bacteria. To elucidate the specific structural role of carotenoids, we analyzed LH2 complexes from Ectothiorhodospira ...The LH2 complex is essential for light harvesting in many photosynthetic bacteria. To elucidate the specific structural role of carotenoids, we analyzed LH2 complexes from Ectothiorhodospira haloalkaliphila with inhibited carotenoid biosynthesis. This approach allowed us to study complexes incorporating the colorless carotenoid phytoene instead of the native, colored pigments. A 1.92 Å cryo-EM reconstruction revealed that phytoene fully substitutes for the native carotenoids while maintaining the octameric symmetry of the complex and the precise arrangement of bacteriochlorophylls. These results demonstrate that the architectural function of carotenoids in LH2 complexes is maintained even when their light-absorption capability is altered, providing new mechanistic insight into the structural basis of pigment-protein interactions in photosynthetic antenna complexes.
History
DepositionJul 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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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 subunit beta
C: Light-harvesting protein B-800/850 alpha chain
D: Light-harvesting protein B:800-850 subunit beta
E: Light-harvesting protein B-800/850 alpha chain
G: Light-harvesting protein B:800-850 subunit beta
H: Light-harvesting protein B-800/850 alpha chain
J: Light-harvesting protein B:800-850 subunit beta
K: Light-harvesting protein B-800/850 alpha chain
M: Light-harvesting protein B:800-850 subunit beta
N: Light-harvesting protein B-800/850 alpha chain
P: Light-harvesting protein B:800-850 subunit beta
Q: Light-harvesting protein B-800/850 alpha chain
S: Light-harvesting protein B:800-850 subunit beta
T: Light-harvesting protein B-800/850 alpha chain
V: Light-harvesting protein B:800-850 subunit beta
W: Light-harvesting protein B-800/850 alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,82948
Polymers106,59316
Non-polymers26,23632
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide
Light-harvesting protein B:800-850 subunit beta


Mass: 5468.237 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Ectothiorhodospira haloalkaliphila ATCC 51935 (bacteria)
References: UniProt: W8KQR0
#2: Protein
Light-harvesting protein B-800/850 alpha chain / Antenna complex alpha/beta subunit domain-containing protein


Mass: 7855.903 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Ectothiorhodospira haloalkaliphila ATCC 51935 (bacteria)
References: UniProt: W8KE12
#3: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-A1MBA / Phytoene / (6~{E},10~{E},14~{Z},16~{Z},18~{E},22~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-2,6,10,14,16,18,22,26,30-nonaene


Mass: 544.936 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H64 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
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: LH2 complex from Ectothiorhodospira haloalkaliphila / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Ectothiorhodospira haloalkaliphila ATCC 51935 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: Preliminary grid screening was performed manually.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm / Cs: 0.01 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12334
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV
Spherical aberration corrector: Microscope was modified with a Cs corrector (CEOS GmbH, Germany).
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1Warp1.0.9particle selection
2PHENIX1.21.2_5419:model refinement
13cryoSPARC4.6.03D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1589688
SymmetryPoint symmetry: C8 (8 fold cyclic)
3D reconstructionResolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 445556 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0088808
ELECTRON MICROSCOPYf_angle_d1.45312336
ELECTRON MICROSCOPYf_dihedral_angle_d15.551616
ELECTRON MICROSCOPYf_chiral_restr0.0851216
ELECTRON MICROSCOPYf_plane_restr0.0131576

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