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- EMDB-62657: EMReady processed EM map of CaRC-LH complex from Chloroflexus aur... -

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Basic information

Entry
Database: EMDB / ID: EMD-62657
TitleEMReady processed EM map of CaRC-LH complex from Chloroflexus aurantiacus
Map data
Sample
  • Complex: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus
KeywordsPHOTOSYNTHESIS
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsGuoqiang H / Shishang D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Integr Plant Biol / Year: 2025
Title: Cryo-EM structure of a minimal reaction center-light-harvesting complex from the phototrophic bacterium Chloroflexus aurantiacus.
Authors: Guoqiang Huang / Shishang Dong / Lin Ma / Lin Li / Jinxin Ju / Mei-Jiao Wang / Jian-Ping Zhang / Sen-Fang Sui / Xiaochun Qin /
Abstract: Photosynthetic organisms have developed various light-harvesting antenna systems to capture light and transfer energy to reaction centers (RCs). Simultaneous utilization of the integral membrane ...Photosynthetic organisms have developed various light-harvesting antenna systems to capture light and transfer energy to reaction centers (RCs). Simultaneous utilization of the integral membrane light-harvesting antenna (LH complex) and the extrinsic antenna (chlorosomes) makes the phototrophic bacterium Chloroflexus (Cfx.) aurantiacus an ideal model for studying filamentous anoxygenic phototrophs (FAPs). Here, we determined the structure of a minimal RC-LH photocomplex from Cfx. aurantiacus J-10-fl (CaRC-LH) at 3.05-Å resolution. The CaRC-LH binds only to seven LH subunits, which form a crescent-shaped antenna surrounding the movable menaquinone-10 (Q) binding site of CaRC. In this complex with minimal LH units, an extra antenna is required to ensure sufficient light-gathering, providing a clear explanation for the presence of chlorosomes in Cfx. aurantiacus. More importantly, the semicircle of the antenna represents a novel RC-LH assembly pattern. Our structure provides a basis for understanding the existence of chlorosomes in Cfx. aurantiacus and the possible assembly pattern of RC-LH.
History
DepositionDec 10, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62657.png

Downloads & links

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Map

FileDownload / File: emd_62657.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 269.856 Å		0.84 Å/pix.
x 320 pix.
= 269.856 Å		0.84 Å/pix.
x 320 pix.
= 269.856 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8433 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-0.18808444 - 17.667860000000001
Average (Standard dev.)0.0064733517 (±0.59783244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 269.856 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62657_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: #2

Fileemd_62657_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus

EntireName: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus
Components
  • Complex: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus

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Supramolecule #1: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus

SupramoleculeName: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)

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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: 7.6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36181
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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