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- EMDB-47675: anti-rhodopsin 1D4 antibody Fab fragment in the complex with tetr... -

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Basic information

Entry
Database: EMDB / ID: EMD-47675
Titleanti-rhodopsin 1D4 antibody Fab fragment in the complex with tetrameric copper storage protein 1
Map dataanti-rhodopsin 1D4 antibody Fab fragment in the complex with tetrameric copper storage protein 1
Sample
  • Complex: anti-rhodopsin 1D4 antibody Fab fragment bound to tetrameric copper storage protein 1 with 1D4 epitope
KeywordsCOPPER BINDING PROTEIN / Csp1 / copper / metal binding protein / antibody Fab fragment / 1D4 / IMMUNE SYSTEM
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 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: Weekie Yao / Adam C Oken / David L Farrens
Abstract: Small proteins can be challenging to study by single-particle cryogenic electron microscopy (cryo-EM) techniques because they have low signal-to-noise ratios, making them difficult to identify and ...Small proteins can be challenging to study by single-particle cryogenic electron microscopy (cryo-EM) techniques because they have low signal-to-noise ratios, making them difficult to identify and analyze. Here we investigated the use of Csp1, a small (∼50 kDa) tetrameric metal-binding protein, to act as a "bio-tag" to help overcome this problem. We find Csp1 is compact, stable, and exhibits enhanced electron scattering and excellent particle contrast in cryo-EM micrographs. As a result, we could determine the structure of Csp1 to 2.98-Å resolution using standard cryo-EM approaches. We also tested if Csp1 could be used as a tag or fiducial to help determine the structure of a protein bound to it. Specifically, we analyzed an epitope-tagged Csp1 bound to a ∼40 kDa Fab fragment from the antibody 1D4. Data from these complexes yielded medium-resolution structures of the complex (5.70 Å) and the bound 1D4 Fab (5.40 Å). These results suggest that, with further optimization, electron-rich Csp1 is a promising bio-tag for use in cryo-EM studies.
History
DepositionNov 1, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47675.png

Downloads & links

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Map

FileDownload / File: emd_47675.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationanti-rhodopsin 1D4 antibody Fab fragment in the complex with tetrameric copper storage protein 1
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
1.94 Å/pix.
x 150 pix.
= 291.6 Å		1.94 Å/pix.
x 150 pix.
= 291.6 Å		1.94 Å/pix.
x 150 pix.
= 291.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.944 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.4
Minimum - Maximum-9.166124 - 10.691514
Average (Standard dev.)0.00326148 (±0.116993874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 291.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47675_msk_1.map
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Half map: Half Map A

Fileemd_47675_half_map_1.map
AnnotationHalf Map A
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Half map: Half Map B

Fileemd_47675_half_map_2.map
AnnotationHalf Map B
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Sample components

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Entire : anti-rhodopsin 1D4 antibody Fab fragment bound to tetrameric copp...

EntireName: anti-rhodopsin 1D4 antibody Fab fragment bound to tetrameric copper storage protein 1 with 1D4 epitope
Components
  • Complex: anti-rhodopsin 1D4 antibody Fab fragment bound to tetrameric copper storage protein 1 with 1D4 epitope

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Supramolecule #1: anti-rhodopsin 1D4 antibody Fab fragment bound to tetrameric copp...

SupramoleculeName: anti-rhodopsin 1D4 antibody Fab fragment bound to tetrameric copper storage protein 1 with 1D4 epitope
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 47 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 58921
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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