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- EMDB-39770: LH2 complex from Ectothiorhodospira haloalkaliphila at near-atomi... -

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Basic information

Entry
Database: EMDB / ID: EMD-39770
TitleLH2 complex from Ectothiorhodospira haloalkaliphila at near-atomic resolution
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: Anhydrorhodovibrin
  • 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 / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / 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 (bacteria) / Ectothiorhodospira haloalkaliphila ATCC 51935 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.7 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: Structure / Year: 2024
Title: Near-atomic cryo-EM structure of the light-harvesting complex LH2 from the sulfur purple bacterium Ectothiorhodospira haloalkaliphila.
Authors: Anna D Burtseva / Timur N Baymukhametov / Maxim A Bolshakov / Zoya К Makhneva / Andrey V Mardanov / Andrey M Tsedilin / Huawei Zhang / Vladimir O Popov / Aleksandr A Ashikhmin / Konstantin M Boyko /
Abstract: Bacteria with the simplest system for solar energy absorption and conversion use various types of light-harvesting complexes for these purposes. Light-harvesting complex 2 (LH2), an important ...Bacteria with the simplest system for solar energy absorption and conversion use various types of light-harvesting complexes for these purposes. Light-harvesting complex 2 (LH2), an important component of the bacterial photosynthetic apparatus, has been structurally well characterized among purple non-sulfur bacteria. In contrast, so far only one high-resolution LH2 structure from sulfur bacteria is known. Here, we report the near-atomic resolution cryoelectron microscopy (cryo-EM) structure of the LH2 complex from the purple sulfur bacterium Ectothiorhodospira haloalkaliphila, which allowed us to determine the predominant polypeptide composition of this complex and the identification of the most probable type of its carotenoid. Comparison of our structure with the only known LH2 complex from a sulfur bacterium revealed severe differences in the overall ring-like organization. Expanding the architectural universe of bacterial light-harvesting complexes, our results demonstrate that, as observed for non-sulfur bacteria, the LH2 complexes of sulfur bacteria may also exhibit various types of spatial organization.
History
DepositionApr 17, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39770.png

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Map

FileDownload / File: emd_39770.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-2.7972505 - 4.536589
Average (Standard dev.)0.00081402477 (±0.061652914)
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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Mask #1

Fileemd_39770_msk_1.map
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Additional map: #2

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Additional map: #1

Fileemd_39770_additional_2.map
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Half map: #2

Fileemd_39770_half_map_1.map
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Half map: #1

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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: Anhydrorhodovibrin
  • 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 (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: Anhydrorhodovibrin

MacromoleculeName: Anhydrorhodovibrin / type: ligand / ID: 4 / Number of copies: 8 / Formula: A1L0S
Molecular weightTheoretical: 566.899 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
Details: The grids were stored under low vacuum conditions and were not specifically pretreated.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN 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: 7346 / Average exposure time: 2.5 sec. / Average electron dose: 52.5 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
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 1.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 324434
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8z4v:
LH2 complex from Ectothiorhodospira haloalkaliphila at near-atomic resolution

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