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- EMDB-21708: Cu(I)-bound Copper Storage Protein BsCsp3 -

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Basic information

Entry
Database: EMDB / ID: EMD-21708
TitleCu(I)-bound Copper Storage Protein BsCsp3
Map dataBsCSP3 Density Map
Sample
  • Complex: BsCsp3, Cu(I) ions
    • Protein or peptide: Csp3
Keywordssmall protein (47 kDa) / Z-contrast enhancement in cryo-EM / copper storage protein / metal binding protein
Function / homologyProtein of unknown function DUF326 / Copper storage protein / Uncharacterized cysteine-rich protein YhjQ-like / Uncharacterized cysteine-rich protein YhjQ
Function and homology information
Biological speciesBacillus subtilis (strain 168) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen JZ / Oken A
Funding support United States, United Kingdom, 2 items
OrganizationGrant numberCountry
Other privateOHSU Startup package United States
Biotechnology and Biological Sciences Research Council (BBSRC)1668110 United Kingdom
CitationJournal: To Be Published
Title: Cu(I)-bound Copper Storage Protein BsCsp3
Authors: Chen JZ / Dennison C
History
DepositionApr 16, 2020-
Header (metadata) releaseApr 21, 2021-
Map releaseApr 21, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wkt
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21708.png

Downloads & links

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Map

FileDownload / File: emd_21708.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBsCSP3 Density Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 96 pix.
= 124.416 Å		1.3 Å/pix.
x 96 pix.
= 124.416 Å		1.3 Å/pix.
x 96 pix.
= 124.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-17.026288999999998 - 24.763655
Average (Standard dev.)0.000000000008222 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 124.416 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2961.2961.296
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z124.416124.416124.416
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-17.02624.7640.000

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Supplemental data

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Mask #1

Fileemd_21708_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BsCSP3 half map - even

Fileemd_21708_half_map_1.map
AnnotationBsCSP3 half map - even
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BsCSP3 half map - odd

Fileemd_21708_half_map_2.map
AnnotationBsCSP3 half map - odd
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BsCsp3, Cu(I) ions

EntireName: BsCsp3, Cu(I) ions
Components
  • Complex: BsCsp3, Cu(I) ions
    • Protein or peptide: Csp3

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Supramolecule #1: BsCsp3, Cu(I) ions

SupramoleculeName: BsCsp3, Cu(I) ions / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 47 KDa

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Macromolecule #1: Csp3

MacromoleculeName: Csp3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 11.853758 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MEQYSEACIE ACIDCMKACN HCFTKCLEES VQHHLSGCIR LDRECADICA LAVKAMQTDS PFMKEICALC ADICEACGTE CGKHDHDHC QACAKACFTC AEQCRSMAA

UniProtKB: Uncharacterized cysteine-rich protein YhjQ

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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

Concentration0.11 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMNaClsodium chloride
20.0 mMHEPESHEPES
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 15 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details: 5 micro-liters of sample loaded, waited 1 second,front + back blotted for 4.5 seconds at force 1 before plunging.
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 90.0 K / Max: 95.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 2212 / Average exposure time: 0.985 sec. / Average electron dose: 40.0 e/Å2
Details: Images were collected at 40 frames per movie. Four movies were collected per stage shift. Frames were collected in super resolution mode at a calibrated pixel size of 0.324 A/pixel.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.1 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 136000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.15 µm / Nominal defocus min: 0.85 µm / Nominal magnification: 130000
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

DetailsThe selected images were dose-weight aligned in MotionCor2 within RELION's framework
Particle selectionNumber selected: 3356122
Details: Automatic particle selections were made in RELION using a previously generated 3D reference and a low picking threshold.
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5fig


Details: A low resolution map was generated using the program PARTICLE from the PDB of 5FIG.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0-beta-2) / Number images used: 121587
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0-beta-2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0-beta-2)
Final 3D classificationNumber classes: 3 / Avg.num./class: 150000 / Software - Name: RELION (ver. 3.0-beta-2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5fig


Chain - Chain ID: A / Chain - Residue range: 4-108 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 46.04 / Target criteria: Correlation coefficient
Output model

PDB-6wkt:
Cu(I)-bound Copper Storage Protein BsCsp3

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