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- PDB-9e7j: Cu-bound tetrameric copper storage protein 1 with anti-rhodopsin ... -

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Open data


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Basic information

Entry
Database: PDB / ID: 9e7j
TitleCu-bound tetrameric copper storage protein 1 with anti-rhodopsin 1D4 epitope
ComponentsFour-helix bundle copper-binding protein
KeywordsMETAL BINDING PROTEIN / tetrameric copper storage protein 1
Function / homologyTwin-arginine translocation signal, Cys-rich four helix bundle protein / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / identical protein binding / Four-helix bundle copper-binding protein
Function and homology information
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsYao, Y. / Oken, A.C. / Farrens, D.L.
Funding support United States, 1items
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, A.C. / Farrens, D.L.
History
DepositionNov 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Four-helix bundle copper-binding protein
B: Four-helix bundle copper-binding protein
C: Four-helix bundle copper-binding protein
D: Four-helix bundle copper-binding protein


Theoretical massNumber of molelcules
Total (without water)45,2854
Polymers45,2854
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Four-helix bundle copper-binding protein


Mass: 11321.135 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: CQW49_12740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D2D105
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cu-bound tetrameric copper storage protein 1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.054 MDa / Experimental value: NO
Source (natural)Organism: Methylosinus trichosporium OB3b (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Buffer componentConc.: 20 mM / Name: HEPES / Formula: C8H18N2O4S
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 1 sec. / Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7020

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Processing

EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4cryoSPARC3.3CTF correctionpatch CTF correction
7PHENIX1.19.2model fitting
9PHENIX1.19.2model refinement
10cryoSPARC3.3initial Euler assignment
11cryoSPARC3.3final Euler assignment
13cryoSPARC3.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6383264
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125008 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 5FJE

5fje


Accession code: 5FJE / Source name: PDB / Type: experimental model

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