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- EMDB-65526: LH2 complex from Ectothiorhodospira haloalkaliphila with inhibite... -

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Basic information

Entry
Database: EMDB / ID: EMD-65526
TitleLH2 complex from Ectothiorhodospira haloalkaliphila with inhibited carotenoid biosynthesis
Map data
Sample
  • Complex: LH2 complex from Ectothiorhodospira haloalkaliphila
    • Protein or peptide: Light-harvesting protein B:800-850 subunit beta
    • Protein or peptide: Light-harvesting protein B-800/850 alpha chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: Phytoene
  • Ligand: water
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.92 Å
AuthorsBurtseva AD / Baymukhametov TN / Popov VO / Ashikhmin AA / Boyko KM
Funding support Russian Federation, 1 items
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 AD / Baymukhametov TN / Popov VO / Ashikhmin AA / Boyko KM
History
DepositionJul 25, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65526.png

Downloads & links

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Map

FileDownload / File: emd_65526.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 400 pix.
= 268. Å		0.67 Å/pix.
x 400 pix.
= 268. Å		0.67 Å/pix.
x 400 pix.
= 268. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.3050765 - 1.8637816
Average (Standard dev.)0.00031934277 (±0.038146213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 268.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_65526_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65526_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65526_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LH2 complex from Ectothiorhodospira haloalkaliphila

EntireName: LH2 complex from Ectothiorhodospira haloalkaliphila
Components
  • Complex: LH2 complex from Ectothiorhodospira haloalkaliphila
    • Protein or peptide: Light-harvesting protein B:800-850 subunit beta
    • Protein or peptide: Light-harvesting protein B-800/850 alpha chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: Phytoene
  • Ligand: water

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Supramolecule #1: LH2 complex from Ectothiorhodospira haloalkaliphila

SupramoleculeName: LH2 complex from Ectothiorhodospira haloalkaliphila / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Ectothiorhodospira haloalkaliphila ATCC 51935 (bacteria)

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Macromolecule #1: Light-harvesting protein B:800-850 subunit beta

MacromoleculeName: Light-harvesting protein B:800-850 subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Ectothiorhodospira haloalkaliphila ATCC 51935 (bacteria)
Molecular weightTheoretical: 5.468237 KDa
SequenceString:
MYDNSISGLT EEQAKEFHEQ FKTTFTVFMV LAAAAHFLVF LWRPFY

UniProtKB: Light-harvesting protein B:800-850 subunit beta

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Macromolecule #2: Light-harvesting protein B-800/850 alpha chain

MacromoleculeName: Light-harvesting protein B-800/850 alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Ectothiorhodospira haloalkaliphila ATCC 51935 (bacteria)
Molecular weightTheoretical: 7.855903 KDa
SequenceString:
MSEYRPSKPS NPRDDWKLWL VVNPGTWLMP ILMAVLVVAL VVHAFVYSND NYNPLTFDAS AEVAAEEAAE

UniProtKB: Antenna complex alpha/beta subunit domain-containing protein

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Macromolecule #3: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 24 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

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Macromolecule #4: Phytoene

MacromoleculeName: Phytoene / type: ligand / ID: 4 / Number of copies: 8 / Formula: A1MBA
Molecular weightTheoretical: 544.936 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 88 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 8
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector (CEOS GmbH, Germany).
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12334 / Average exposure time: 2.5 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1589688
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 445556
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9w1c:
LH2 complex from Ectothiorhodospira haloalkaliphila with inhibited carotenoid biosynthesis

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