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- EMDB-52514: FCPa region focused map -

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Basic information

Entry
Database: EMDB / ID: EMD-52514
TitleFCPa region focused map
Map dataFCPa region map
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: 2.17 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: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJan 10, 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_52514.png

Downloads & links

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Map

FileDownload / File: emd_52514.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFCPa region map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 500 pix.
= 365. Å		0.73 Å/pix.
x 500 pix.
= 365. Å		0.73 Å/pix.
x 500 pix.
= 365. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.00873101 - 0.029481359
Average (Standard dev.)-0.00007497786 (±0.0005385403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 365.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_52514_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_52514_half_map_2.map
Annotationhalf 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-#19
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: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. v5.0.0b)
Details: An individual local mask 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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