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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: To Be Published
Title: Structure of the LH2 complex from Ectothiorhodospira haloalkaliphila with inhibited carotenoid biosynthesis
Authors: Burtseva, A.D. / Baymukhametov, T.N. / Popov, V.O. / Ashikhmin, A.A. / Boyko, K.M.
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
Revision 1.0Oct 22, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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