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- EMDB-6758: Local map for the core region of the phycobilisome from the red a... -

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Basic information

Entry
Database: EMDB / ID: 6758
TitleLocal map for the core region of the phycobilisome from the red alga Griffithsia pacifica
Map datalocal map for core region of the red alga Griffithsia pacifica phycobilisome
Samplephycobilisome from the red alga Griffithsia pacifica:
SourceGriffithsia pacifica (eukaryote)
Methodsingle particle reconstruction / cryo EM / 3.43 Å resolution
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
DateDeposition: Jun 12, 2017 / Header (metadata) release: Oct 25, 2017 / Map release: Oct 25, 2017 / Last update: Nov 15, 2017

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Structure visualization

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

Downloads & links

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Map

Fileemd_6758.map.gz (map file in CCP4 format, 702465 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
560 pix
1.32 Å/pix.
= 739.2 Å
560 pix
1.32 Å/pix.
= 739.2 Å
560 pix
1.32 Å/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
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.12692031 - 0.20864116
Average (Standard dev.)2.103249E-5 (0.00809662)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions560560560
Origin000
Limit559559559
Spacing560560560
CellA=B=C: 739.2 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-0.1270.2090.000

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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 / Number of components: 1
MassExperimental: 16.8 MDa

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Component #1: protein, phycobilisome from the red alga Griffithsia pacifica

ProteinName: phycobilisome from the red alga Griffithsia pacifica / Recombinant expression: No
MassExperimental: 16.8 MDa
SourceSpecies: Griffithsia pacifica (eukaryote)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7
Support filmThe grid was coated with holy carbon
VitrificationCryogen name: ETHANE / Temperature: 289.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 8 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 22500 X (nominal), 22500 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400 - 2300 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 53403
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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