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- EMDB-1642: Structure of chlorosomes from the green filamentous bacterium Chl... -

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Basic information

Entry
Database: EMDB / ID: EMD-1642
TitleStructure of chlorosomes from the green filamentous bacterium Chloroflexus aurantiacus
Map dataThis is a tomogram of an individual Chloroflexus aurantiacus chlorosome.
Sample
  • Sample: A chlorosome of Chloroflexus aurantiacus
  • Organelle or cellular component: Chlorosome
KeywordsChlorosome / light-harvesting complex / Chloroflexus
Biological speciesChloroflexus aurantiacus (bacteria)
Methodsubtomogram averaging / cryo EM
AuthorsPsencik J / Collins AM / Liljeroos L / Torkkeli M / Laurinmaki P / Ansink HM / Ikonen TP / Serimaa RE / Blankenship RE / Tuma R / Butcher SJ
CitationJournal: J Bacteriol / Year: 2009
Title: Structure of chlorosomes from the green filamentous bacterium Chloroflexus aurantiacus.
Authors: Jakub Psencík / Aaron M Collins / Lassi Liljeroos / Mika Torkkeli / Pasi Laurinmäki / Hermanus M Ansink / Teemu P Ikonen / Ritva E Serimaa / Robert E Blankenship / Roman Tuma / Sarah J Butcher /
Abstract: The green filamentous bacterium Chloroflexus aurantiacus employs chlorosomes as photosynthetic antennae. Chlorosomes contain bacteriochlorophyll aggregates and are attached to the inner side of a ...The green filamentous bacterium Chloroflexus aurantiacus employs chlorosomes as photosynthetic antennae. Chlorosomes contain bacteriochlorophyll aggregates and are attached to the inner side of a plasma membrane via a protein baseplate. The structure of chlorosomes from C. aurantiacus was investigated by using a combination of cryo-electron microscopy and X-ray diffraction and compared with that of Chlorobi species. Cryo-electron tomography revealed thin chlorosomes for which a distinct crystalline baseplate lattice was visualized in high-resolution projections. The baseplate is present only on one side of the chlorosome, and the lattice dimensions suggest that a dimer of the CsmA protein is the building block. The bacteriochlorophyll aggregates inside the chlorosome are arranged in lamellae, but the spacing is much greater than that in Chlorobi species. A comparison of chlorosomes from different species suggested that the lamellar spacing is proportional to the chain length of the esterifying alcohols. C. aurantiacus chlorosomes accumulate larger quantities of carotenoids under high-light conditions, presumably to provide photoprotection. The wider lamellae allow accommodation of the additional carotenoids and lead to increased disorder within the lamellae.
History
DepositionAug 18, 2009-
Header (metadata) releaseAug 19, 2009-
Map releaseSep 3, 2009-
UpdateSep 9, 2011-
Current statusSep 9, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 67.030927835
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 67.030927835
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1642.jpg

Downloads & links

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Map

FileDownload / File: emd_1642.map.gz / Format: CCP4 / Size: 335 KB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationThis is a tomogram of an individual Chloroflexus aurantiacus chlorosome.
Voxel sizeX=Y=Z: 23 Å
Density
Contour LevelBy AUTHOR: 58.700000000000003 / Movie #1: 67.0309278
Minimum - Maximum-171.0 - 249.0
Average (Standard dev.)1.77992 (±31.613600000000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions745940
Spacing745940
CellA: 1702 Å / B: 1357 Å / C: 920 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z232323
M x/y/z745940
origin x/y/z0.0000.0000.000
length x/y/z1702.0001357.000920.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS597440
D min/max/mean-171.000249.0001.780

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Supplemental data

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Sample components

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Entire : A chlorosome of Chloroflexus aurantiacus

EntireName: A chlorosome of Chloroflexus aurantiacus
Components
  • Sample: A chlorosome of Chloroflexus aurantiacus
  • Organelle or cellular component: Chlorosome

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Supramolecule #1000: A chlorosome of Chloroflexus aurantiacus

SupramoleculeName: A chlorosome of Chloroflexus aurantiacus / type: sample / ID: 1000 / Oligomeric state: Monomeric / Number unique components: 1

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Supramolecule #1: Chlorosome

SupramoleculeName: Chlorosome / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Chlorosome / Oligomeric state: Monomeric / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Chloroflexus aurantiacus (bacteria) / Cell: Chloroflexus aurantiacus

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferpH: 8 / Details: sample was dialyzed against water
GridDetails: Quantifoil R2/2 holey carbon film, copper grid 400 mesh
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Homemade plunger / Method: Blot for 1.5 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 25840 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 25840
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -64 ° / Tilt series - Axis1 - Max angle: 64 °
TemperatureMin: 93 K / Max: 103 K / Average: 93 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 80,000 times magnification
DetailsLow-dose illumination
DateFeb 15, 2008
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 1.50 µm / Number real images: 65 / Average electron dose: 160 e/Å2 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Software - Name: IMOD
DetailsParticles were selected manually. Average number of tilts used in the 3D reconstructions: 65. Average tomographic tilt angle increment: 2.

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