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- EMDB-6759: Local map for the Rd region of the phycobilisome from the red alg... -

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Basic information

Entry
Database: EMDB / ID: EMD-6759
TitleLocal map for the Rd region of the phycobilisome from the red alga Griffithsia pacifica
Map data
Sample
  • Complex: phycobilisome from the red alga Griffithsia pacifica
Biological speciesGriffithsia pacifica (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsZhang J / Ma JF / Sun S / Sui SF
CitationJournal: Nature / Year: 2017
Title: Structure of phycobilisome from the red alga Griffithsia pacifica.
Authors: Jun Zhang / Jianfei Ma / Desheng Liu / Song Qin / Shan Sun / Jindong Zhao / Sen-Fang Sui /
Abstract: Life on Earth depends on photosynthesis for its conversion of solar energy to chemical energy. Photosynthetic organisms have developed a variety of light-harvesting systems to capture sunlight. The ...Life on Earth depends on photosynthesis for its conversion of solar energy to chemical energy. Photosynthetic organisms have developed a variety of light-harvesting systems to capture sunlight. The largest light-harvesting complex is the phycobilisome (PBS), the main light-harvesting antenna in cyanobacteria and red algae. It is composed of phycobiliproteins and linker proteins but the assembly mechanisms and energy transfer pathways of the PBS are not well understood. Here we report the structure of a 16.8-megadalton PBS from a red alga at 3.5 Å resolution obtained by single-particle cryo-electron microscopy. We modelled 862 protein subunits, including 4 linkers in the core, 16 rod-core linkers and 52 rod linkers, and located a total of 2,048 chromophores. This structure reveals the mechanisms underlying specific interactions between linkers and phycobiliproteins, and the formation of linker skeletons. These results provide a firm structural basis for our understanding of complex assembly and the mechanisms of energy transfer within the PBS.
History
DepositionJun 12, 2017-
Header (metadata) releaseOct 25, 2017-
Map releaseOct 25, 2017-
UpdateNov 15, 2017-
Current statusNov 15, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6759.png

Downloads & links

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Map

FileDownload / File: emd_6759.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 560 pix.
= 739.2 Å		1.32 Å/pix.
x 560 pix.
= 739.2 Å		1.32 Å/pix.
x 560 pix.
= 739.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.07673699 - 0.12976742
Average (Standard dev.)0.00009038097 (±0.005874991)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 739.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z739.200739.200739.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-0.0770.1300.000

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Supplemental data

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Sample components

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Entire : phycobilisome from the red alga Griffithsia pacifica

EntireName: phycobilisome from the red alga Griffithsia pacifica
Components
  • Complex: phycobilisome from the red alga Griffithsia pacifica

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Supramolecule #1: phycobilisome from the red alga Griffithsia pacifica

SupramoleculeName: phycobilisome from the red alga Griffithsia pacifica / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Griffithsia pacifica (eukaryote)
Molecular weightExperimental: 16.8 MDa

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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

Concentration1 mg/mL
BufferpH: 7
GridModel: Qiagen / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: The grid was coated with holy carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.3 µm / Calibrated defocus min: 1.4 µm / Calibrated magnification: 22500 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 22500
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

Startup modelType of model: OTHER / Details: produced by spider
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53403
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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