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- EMDB-47275: Light Harvesting complex 3 (LH3), B800-B820, of Rhodoblastus (Rbl... -

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Basic information

Entry
Database: EMDB / ID: EMD-47275
TitleLight Harvesting complex 3 (LH3), B800-B820, of Rhodoblastus (Rbl.) acidophilus strain 7750
Map dataLight Harvesting complex 3 (LH3), B800-B820, of Rhodoblastus (Rbl.) acidophilus strain 7750
Sample
  • Complex: Nonameric complex of the low-light induced Light Harvesting complex 3 (LH3)
    • Protein or peptide: Light-harvesting protein B-800/820 alpha chain
    • Protein or peptide: Light-harvesting protein B-800/820 beta-2 chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: LAURYL DIMETHYLAMINE-N-OXIDE
  • Ligand: 1,2-Dihydro-psi,psi-caroten-1-ol
  • Ligand: DODECYL-BETA-D-MALTOSIDE
KeywordsLight Harvesting / acclimation / stress / PHOTOSYNTHESIS
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
Light-harvesting protein B-800/820 alpha chain / Light-harvesting protein B-800/820 beta-2 chain
Similarity search - Component
Biological speciesRhodoblastus acidophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsHarris D / Schlau-Cohen GS
Funding support United States, 2 items
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 GP / Feibig OC / Schlau-Cohen GS
History
DepositionOct 10, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47275.png

Downloads & links

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Map

FileDownload / File: emd_47275.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLight Harvesting complex 3 (LH3), B800-B820, of Rhodoblastus (Rbl.) acidophilus strain 7750
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 380 pix.
= 248.52 Å		0.65 Å/pix.
x 380 pix.
= 248.52 Å		0.65 Å/pix.
x 380 pix.
= 248.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.06
Minimum - Maximum-0.20645632 - 21.2941
Average (Standard dev.)-0.040562715 (±0.57616717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 248.51999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_47275_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_47275_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nonameric complex of the low-light induced Light Harvesting compl...

EntireName: Nonameric complex of the low-light induced Light Harvesting complex 3 (LH3)
Components
  • Complex: Nonameric complex of the low-light induced Light Harvesting complex 3 (LH3)
    • Protein or peptide: Light-harvesting protein B-800/820 alpha chain
    • Protein or peptide: Light-harvesting protein B-800/820 beta-2 chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: LAURYL DIMETHYLAMINE-N-OXIDE
  • Ligand: 1,2-Dihydro-psi,psi-caroten-1-ol
  • Ligand: DODECYL-BETA-D-MALTOSIDE

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Supramolecule #1: Nonameric complex of the low-light induced Light Harvesting compl...

SupramoleculeName: Nonameric complex of the low-light induced Light Harvesting complex 3 (LH3)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rhodoblastus acidophilus (bacteria) / Strain: 7750
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Light-harvesting protein B-800/820 alpha chain

MacromoleculeName: Light-harvesting protein B-800/820 alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Rhodoblastus acidophilus (bacteria) / Strain: 7750
Molecular weightTheoretical: 5.113006 KDa
SequenceString:
(FME)NQGKIWTVV NPAVGLPLLL GSVAITALLV HLAVLTHTTW FPAFQQGG

UniProtKB: Light-harvesting protein B-800/820 alpha chain

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Macromolecule #2: Light-harvesting protein B-800/820 beta-2 chain

MacromoleculeName: Light-harvesting protein B-800/820 beta-2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Rhodoblastus acidophilus (bacteria)
Molecular weightTheoretical: 4.553242 KDa
SequenceString:
AVLSPEQSEE LHKYVIDGAR AFLGIALVAH FLAFSLTPWL H

UniProtKB: Light-harvesting protein B-800/820 beta-2 chain

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Macromolecule #3: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 27 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #4: LAURYL DIMETHYLAMINE-N-OXIDE

MacromoleculeName: LAURYL DIMETHYLAMINE-N-OXIDE / type: ligand / ID: 4 / Number of copies: 9 / Formula: LDA
Molecular weightTheoretical: 229.402 Da
Chemical component information

ChemComp-LDA:
LAURYL DIMETHYLAMINE-N-OXIDE / LDAO, detergent*YM

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Macromolecule #5: 1,2-Dihydro-psi,psi-caroten-1-ol

MacromoleculeName: 1,2-Dihydro-psi,psi-caroten-1-ol / type: ligand / ID: 5 / Number of copies: 9 / Formula: IRM
Molecular weightTheoretical: 554.888 Da
Chemical component information

ChemComp-IRM:
1,2-Dihydro-psi,psi-caroten-1-ol

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Macromolecule #6: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 6 / Number of copies: 9 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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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

Concentration0.75 mg/mL
BufferpH: 7.8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 43.37 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49453
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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