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- EMDB-8750: GroEL using cryoEM -

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Basic information

Entry
Database: EMDB / ID: 8750
TitleGroEL using cryoEM
SampleWild type GroEL
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataGroEL
Methodsingle particle reconstruction, at 3.5 Å resolution
AuthorsRoh SH / Hryc CF / Jeong HH / Fei X / Jakana J / Lorimer GH / Chiu W
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 8259-8264

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 8259-8264 Yorodumi Papers
Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM.
Soung-Hun Roh / Corey F Hryc / Hyun-Hwan Jeong / Xue Fei / Joanita Jakana / George H Lorimer / Wah Chiu

Validation ReportPDB-ID: 5w0s

SummaryFull reportAbout validation report
DateDeposition: May 31, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Aug 9, 2017 / Last update: Sep 20, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5w0s
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8750.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.23 Å/pix.
= 295.2 Å
240 pix
1.23 Å/pix.
= 295.2 Å
240 pix
1.23 Å/pix.
= 295.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.23 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.11138689 - 0.20425552
Average (Standard dev.)0.00017152682 (0.011501166)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin000
Limit239239239
Spacing240240240
CellA=B=C: 1 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z295.200295.200295.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1110.2040.000

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Supplemental data

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Sample components

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Entire Wild type GroEL

EntireName: Wild type GroEL / Number of components: 3

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Component #1: protein, Wild type GroEL

ProteinName: Wild type GroEL / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, 60 kDa chaperonin

ProteinName: 60 kDa chaperonin / Recombinant expression: No
MassTheoretical: 55.14802 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #3: ligand, water

LigandName: water / Number of Copies: 107 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml / pH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D7 (2*7 fold dihedral) / Number of projections: 37367
3D reconstructionSoftware: RELION / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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