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- EMDB-4185: Human GroEL obtained by grid-blotting from blue native PAGE -

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Basic information

Entry
Database: EMDB / ID: 4185
TitleHuman GroEL obtained by grid-blotting from blue native PAGE
Map dataGrid blotted from blue native PAGE human GroEL
SampleGroEL only:
SourceHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / 25 Å resolution
AuthorsKirykowicz AM / Woodward JD
CitationJournal: To Be Published
Title: Human GroEL obtained by grid-blotting from blue native PAGE
Authors: Kirykowicz AM / Woodward JD
DateDeposition: Nov 30, 2017 / Header (metadata) release: Dec 13, 2017 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.45
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4185.map.gz (map file in CCP4 format, 1049 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
4.22 Å/pix.
= 270.08 Å
64 pix
4.22 Å/pix.
= 270.08 Å
64 pix
4.22 Å/pix.
= 270.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.22 Å
Density
Contour Level:2.45 (by author), 2.45 (movie #1):
Minimum - Maximum-3.3466055 - 6.095054
Average (Standard dev.)0.000000006981233 (1.0)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin-32.0-32.0-32.0
Limit31.031.031.0
Spacing646464
CellA=B=C: 270.08 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.224.224.22
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z270.080270.080270.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-3.3476.0950.000

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Supplemental data

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Sample components

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Entire GroEL only

EntireName: GroEL only / Details: Obtained from Sigma-Aldrich / Number of components: 1

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Component #1: protein, GroEL only

ProteinName: GroEL only / Details: Obtained from Sigma-Aldrich / Recombinant expression: No
MassExperimental: 840 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: Diluted in 50 mM Tris-HCl, 200 mM NaCl (pH 8.0). 1-5 ug of GroEL run on blue native page: Anode buffer: 25 mM Imidazole Cathode buffer A: 50 mM Tricine, 7.5 mM Imidazole, 0.02% Coomassie G250 (pH 7.0) Cathode buffer B: 50 mM Tricine, 7.5 mM Imidazole, 0.002% Coomassie G250 (pH 7.0)
pH: 7
Staining1-5 ug of groEL was run on a blue native PAGE gel. Sample was transferred to grid by grid blotting procedure and washed/stained with 2% UA.
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: OTHER
LensMagnification: 50000.0 X (nominal) / Cs: 1.2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D7 (2*7 fold dihedral) / Number of projections: 463
3D reconstructionResolution: 25 Å / Resolution method: FSC 0.5 CUT-OFF / Details: EMAN procedure
Euler angles: EMAN procedure: 5 iteration of 10 degrees (19 classes generated), 5 iterations of 8 degrees (23 classes generated), 10 iterations of 5 degrees (61 classes generated), and 6 iterations of 3 degrees (155 classes generated)

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