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- EMDB-47674: Cu-bound tetrameric copper storage protein 1 (Csp1) in Csp1-1D4 c... -

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Basic information

Entry
Database: EMDB / ID: EMD-47674
TitleCu-bound tetrameric copper storage protein 1 (Csp1) in Csp1-1D4 complex
Map dataCu-bound tetrameric copper storage protein 1 (Csp1) in Csp1-1D4 complex
Sample
  • Complex: Tetrameric structure of copper structure protein 1, Csp1, with copper, bound by 1D4 Fab fragment
KeywordsCOPPER BINDING PROTEIN / Csp1 / copper / metal binding protein
Biological speciesMethylosinus trichosporium OB3b (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.09 Å
AuthorsOken AC / Yao Y / Farrens DL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01 EY029343 United States
CitationJournal: Biophys.J. / Year: 2025
Title: A novel "bio-tag" for cryo-EM studies based on the small, electron-dense protein Csp1
Authors: Yao W / Oken AC / Farrens DL
History
DepositionNov 1, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47674.png

Downloads & links

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Map

FileDownload / File: emd_47674.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCu-bound tetrameric copper storage protein 1 (Csp1) in Csp1-1D4 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 300 pix.
= 291.6 Å		0.97 Å/pix.
x 300 pix.
= 291.6 Å		0.97 Å/pix.
x 300 pix.
= 291.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.972 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.85
Minimum - Maximum-2.8148463 - 6.018082
Average (Standard dev.)0.0013301221 (±0.06479971)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 291.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47674_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_47674_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_47674_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrameric structure of copper structure protein 1, Csp1, with co...

EntireName: Tetrameric structure of copper structure protein 1, Csp1, with copper, bound by 1D4 Fab fragment
Components
  • Complex: Tetrameric structure of copper structure protein 1, Csp1, with copper, bound by 1D4 Fab fragment

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Supramolecule #1: Tetrameric structure of copper structure protein 1, Csp1, with co...

SupramoleculeName: Tetrameric structure of copper structure protein 1, Csp1, with copper, bound by 1D4 Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Methylosinus trichosporium OB3b (bacteria)
Molecular weightTheoretical: 54 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

BufferpH: 7.5 / Component - Concentration: 20.0 mM / Component - Formula: C8H18N2O4S / Component - Name: HEPES
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1926 / Average exposure time: 2.0 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1181918
CTF correctionSoftware - Name: cryoSPARC (ver. 3.1) / Software - details: Patch CTF correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5fje

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 47664
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1) / Software - details: Local refinement
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.1) / Software - details: Reference free classification
FSC plot (resolution estimation)

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