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- EMDB-62901: PSI trimer of Synechocystis sp. PCC 6803 -

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Basic information

Entry
Database: EMDB / ID: EMD-62901
TitlePSI trimer of Synechocystis sp. PCC 6803
Map data
Sample
  • Complex: PSI trimer of Synechocystis sp. PCC 6803
KeywordsPhotosystem I / cyanobacteria / PHOTOSYNTHESIS
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsShen LL / Han GY
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200199 China
National Natural Science Foundation of China (NSFC)32422005 China
CitationJournal: Arch Otolaryngol / Year: 1980
Title: The efficacy of steroids in the treatment of idiopathic sudden hearing loss. A double-blind clinical study.
Abstract: Double-blind studies were conducted for the treatment of idiopathic sudden hearing loss (ISHL) with oral steroids. The condition was defined as not less than a 30-dB loss over three contiguous ...Double-blind studies were conducted for the treatment of idiopathic sudden hearing loss (ISHL) with oral steroids. The condition was defined as not less than a 30-dB loss over three contiguous frequencies in three days or less. Follow-up audiograms were obtained four weeks and three months later. Specific audiologic guidelines for the assessment of hearing recovery were used to ensure objectivity. Steroids had a statistically significant effect on the recovery of hearing in patients with moderate hearing losses. The nature of the hearing loss and its susceptibility to improvement with steroid therapy lend support to the hypothesis that viral cochlitis is the primary cause of ISHL.
History
DepositionDec 30, 2024-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62901.png

Downloads & links

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Map

FileDownload / File: emd_62901.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0467
Minimum - Maximum-0.094199084 - 0.1959785
Average (Standard dev.)0.00027805776 (±0.00808782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62901_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_62901_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 trimer of Synechocystis sp. PCC 6803

EntireName: PSI trimer of Synechocystis sp. PCC 6803
Components
  • Complex: PSI trimer of Synechocystis sp. PCC 6803

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Supramolecule #1: PSI trimer of Synechocystis sp. PCC 6803

SupramoleculeName: PSI trimer of Synechocystis sp. PCC 6803 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 301586
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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