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- EMDB-52499: FCPe region focused map -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52499
TitleFCPe region focused map
Map data
Sample
  • Complex: PSI super complex from Chrome velia
KeywordsPhotosynthesis / Photosystem I / PSI-FCP complex / Chrome velia / Cryo-EM.
Biological speciesChromera velia (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.05 Å
AuthorsYuan X / Qian P / Sobotka R / Naschberger A
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)Synergy Award 854126European Union
CitationJournal: To Be Published
Title: Cryo-EM structure of PSI super complex from Chromera. velia
Authors: Yuan X / Qian P / Sobotka R / Naschberger A
History
DepositionJan 9, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52499.png

Downloads & links

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Map

FileDownload / File: emd_52499.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 500 pix.
= 1025. Å		2.05 Å/pix.
x 500 pix.
= 1025. Å		2.05 Å/pix.
x 500 pix.
= 1025. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.007475824 - 0.025113298
Average (Standard dev.)-0.000075370604 (±0.00057548285)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 1025.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52499_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52499_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PSI super complex from Chrome velia

EntireName: PSI super complex from Chrome velia
Components
  • Complex: PSI super complex from Chrome velia

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Supramolecule #1: PSI super complex from Chrome velia

SupramoleculeName: PSI super complex from Chrome velia / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Details: A complex containing PSI as a core with other components for example PsaA-, PsaB, Psa
Source (natural)Organism: Chromera velia (eukaryote) / Strain: RM12
Molecular weightTheoretical: 654.4 KDa

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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

Concentration0.8 mg/mL
BufferpH: 6.5 / Component - Concentration: 20.0 mM / Component - Formula: C6H13NO4S / Component - Name: MES
Details: 20 mM MES pH 6.5, 0.15M NaCl and 0.01% Lauryl maltose neopentyl glycol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Details: Blotting time 2.5 sec..
DetailsProtein sample in buffer solution of 20 mM MES pH 6.5, 0.15M NaCl and 0.01% Lauryl maltose neopentyl glycol

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 79.0 K / Max: 81.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 32897 / Average exposure time: 3.16 sec. / Average electron dose: 40.0 e/Å2
Details: Two dataset were collected and merged together during data processing.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
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

DetailsMotion correction and CTF estimation were performed on the raw data in cryoSPARC's Live session
Particle selectionNumber selected: 5807142 / Details: Blob picking was selected initially.
CTF correctionSoftware - Name: cryoSPARC (ver. v4.5.3)
Details: CTF estimation were performed on the raw data in cryoSPARC's Live session
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Ab initio reconstruction was used to create initial models for both datasets.
Details: Data for Ab initio reconstruction were obtained from the dataset after two rounds 2d classification.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. v5.0.0b)
Details: An individual local mask at FCPe region was created using ChimeraX's map eraser tool
Number images used: 532882
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v4.5.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v4.5.3)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. v4.5.3)
Details: For Dataset 1, two rounds of heterogeneous refinement were performed using five classes. Dataset 2 underwent eight rounds of heterogeneous refinement using five classes.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 21.6 / Target criteria: CCC in ChimeraX

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