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- EMDB-6422: CryoEM structure of GroEL -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-6422
TitleCryoEM structure of GroEL
Map dataCryoEM structure of GroEL
Sample
  • Sample: Wild type GroEL
  • Protein or peptide: GroEL
KeywordsGroEL
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsRoh SH / Hryc C / Chiu W
CitationJournal: To Be Published
Title: CryoEM of GroEL
Authors: Roh SH / Hryc C / Chiu W
History
DepositionAug 10, 2015-
Header (metadata) releaseSep 2, 2015-
Map releaseSep 2, 2015-
UpdateSep 16, 2015-
Current statusSep 16, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6422.gif

Downloads & links

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Map

FileDownload / File: emd_6422.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of GroEL
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-8.8404007 - 16.466403960000001
Average (Standard dev.)0.0 (±1.0014087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z256.800256.800256.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-8.84016.466-0.000

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Supplemental data

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Supplemental map: emd 6422 additional 1.map

Fileemd_6422_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 6422 half map 1.map

Fileemd_6422_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 6422 half map 2.map

Fileemd_6422_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Wild type GroEL

EntireName: Wild type GroEL
Components
  • Sample: Wild type GroEL
  • Protein or peptide: GroEL

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Supramolecule #1000: Wild type GroEL

SupramoleculeName: Wild type GroEL / type: sample / ID: 1000 / Oligomeric state: 14-mer / Number unique components: 1
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa

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Macromolecule #1: GroEL

MacromoleculeName: GroEL / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration1.0 mg/mL
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: LEICA EM GP / Method: Blot once for 5 seconds.

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Electron microscopy

MicroscopeJEOL 3200FS
TemperatureAverage: 86 K
Specialist opticsEnergy filter - Name: in-column omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 25.0 eV
DateAug 8, 2014
Image recordingCategory: CCD / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Number real images: 300 / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 59800 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.3 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

CTF correctionDetails: particle-based
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: OTHER / Software - Name: EMAN2, RELION / Number images used: 40000

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