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- EMDB-31409: Local map for Hd region of the red alga Porphyridium purpureum ph... -

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Basic information

Entry
Database: EMDB / ID: EMD-31409
TitleLocal map for Hd region of the red alga Porphyridium purpureum phycobilisome in Middle Light
Map dataHd
Sample
  • Complex: phycobilisome
Keywordsphycobilisome / light-harvesting complex / photosynthesis
Biological speciesPorphyridium purpureum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.09 Å
AuthorsMa JF / Sui S-F
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670745 China
National Natural Science Foundation of China (NSFC)31861143048 China
CitationJournal: Commun Biol / Year: 2023
Title: The structural basis for light acclimation in phycobilisome light harvesting systems systems in Porphyridium purpureum
Authors: Dodson EJ / Ma J / Suissa Szlejf M / Maroudas-Sklare N / Paltiel Y / Adir N / Sun S / Sui SF / Keren N
History
DepositionJun 8, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31409.png

Downloads & links

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Map

FileDownload / File: emd_31409.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHd
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 580 pix.
= 618.28 Å		1.07 Å/pix.
x 580 pix.
= 618.28 Å		1.07 Å/pix.
x 580 pix.
= 618.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.066 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.0064005735 - 0.018266689
Average (Standard dev.)0.0000106896205 (±0.00026164908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions580580580
Spacing580580580
CellA=B=C: 618.2801 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : phycobilisome

EntireName: phycobilisome
Components
  • Complex: phycobilisome

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Supramolecule #1: phycobilisome

SupramoleculeName: phycobilisome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 14700 kDa/nm

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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
Component:
ConcentrationFormula
0.75 mol/LNa2HPO4
0.75 mol/LKH2PO4
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 18 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF Quantum ER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 2 / Number real images: 6438 / Average exposure time: 8.2 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.3000000000000003 µm / Calibrated defocus min: 1.3 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 130000
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: 315046
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kgx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1beta) / Number images used: 87399
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1beta)
Final 3D classificationNumber classes: 5 / Avg.num./class: 87399 / Software - Name: RELION (ver. 3.1beta)

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Atomic model buiding 1

Initial modelPDB ID:

6kgx


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 62.05 / Target criteria: 0,99

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