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- PDB-9dwz: Light Harvesting complex 3 (LH3), B800-B820, of Rhodoblastus (Rbl... -

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Basic information

Entry
Database: PDB / ID: 9dwz
TitleLight Harvesting complex 3 (LH3), B800-B820, of Rhodoblastus (Rbl.) acidophilus strain 7750
Components(Light-harvesting protein B-800/820 ...) x 2
KeywordsPHOTOSYNTHESIS / Light Harvesting / acclimation / stress
Function / homology
Function and homology information


organelle inner membrane / 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 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 / 1,2-Dihydro-psi,psi-caroten-1-ol / Light-harvesting protein B-800/820 alpha chain / Light-harvesting protein B-800/820 beta-2 chain
Similarity search - Component
Biological speciesRhodoblastus acidophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsHarris, D. / Schlau-Cohen, G.S.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0018097 United States
National Science Foundation (NSF, United States)DMR-1419807 United States
CitationJournal: To Be Published
Title: Robust light-harvesting properties upon chromatic acclimation in purple bacteria
Authors: Wang, D. / Harris, D. / Chuang, C. / Schmidt, G.P. / Feibig, O.C. / Schlau-Cohen, G.S.
History
DepositionOct 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 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

Downloads & links

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Assembly

Deposited unit
A: Light-harvesting protein B-800/820 alpha chain
B: Light-harvesting protein B-800/820 beta-2 chain
C: Light-harvesting protein B-800/820 alpha chain
D: Light-harvesting protein B-800/820 beta-2 chain
E: Light-harvesting protein B-800/820 alpha chain
F: Light-harvesting protein B-800/820 beta-2 chain
G: Light-harvesting protein B-800/820 alpha chain
H: Light-harvesting protein B-800/820 beta-2 chain
I: Light-harvesting protein B-800/820 alpha chain
J: Light-harvesting protein B-800/820 beta-2 chain
K: Light-harvesting protein B-800/820 alpha chain
L: Light-harvesting protein B-800/820 beta-2 chain
M: Light-harvesting protein B-800/820 alpha chain
N: Light-harvesting protein B-800/820 beta-2 chain
O: Light-harvesting protein B-800/820 alpha chain
P: Light-harvesting protein B-800/820 beta-2 chain
Q: Light-harvesting protein B-800/820 alpha chain
R: Light-harvesting protein B-800/820 beta-2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,26172
Polymers86,99618
Non-polymers36,26554
Water00
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

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Light-harvesting protein B-800/820 ... , 2 types, 18 molecules ACEGIKMOQBDFHJLNPR

#1: Protein/peptide
Light-harvesting protein B-800/820 alpha chain / Antenna pigment protein alpha chain


Mass: 5113.006 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rhodoblastus acidophilus (bacteria) / Strain: 7750 / References: UniProt: P35090
#2: Protein/peptide
Light-harvesting protein B-800/820 beta-2 chain / Antenna pigment protein beta-2 chain


Mass: 4553.242 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rhodoblastus acidophilus (bacteria) / Variant: 7750 / References: UniProt: P35096

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Sugars , 1 types, 9 molecules

#6: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 3 types, 45 molecules

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


Mass: 911.504 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical
ChemComp-IRM / 1,2-Dihydro-psi,psi-caroten-1-ol / Rhodopin / (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-6,8,10,12,14,16,18,20,22,24,26,30-dodecaen-2-ol


Mass: 554.888 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C40H58O / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: Nonameric complex of the low-light induced Light Harvesting complex 3 (LH3)
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.13 MDa / Experimental value: NO
Source (natural)Organism: Rhodoblastus acidophilus (bacteria) / Strain: 7750
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: M13
Buffer solutionpH: 7.8
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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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 recordingAverage exposure time: 1 sec. / Electron dose: 43.37 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49453 / Symmetry type: POINT

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