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- EMDB-5001: Native, unliganded GroEL, D7 symmetrized, 4.2 A resolution 0.5 cr... -

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Entry
Database: EMDB / ID: 5001
TitleNative, unliganded GroEL, D7 symmetrized, 4.2 A resolution 0.5 criterion
Map dataD7 structure of GroEL at 4.2 Angstrom resolution
SampleNative unliganded GroEL, residual ADP:
GroEL
Keywordsgroel / chaperonin / chaperone / backbone trace / eman / single particle
Function / homologyChaperonin Cpn60, conserved site / GroEL-like equatorial domain superfamily / Chaperonins cpn60 signature. / Chaperonin Cpn60/TCP-1 family / Chaperonin Cpn60 / TCP-1/cpn60 chaperonin family / GroEL-like apical domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / in:IPR012723: / GroEL-GroES complex ...Chaperonin Cpn60, conserved site / GroEL-like equatorial domain superfamily / Chaperonins cpn60 signature. / Chaperonin Cpn60/TCP-1 family / Chaperonin Cpn60 / TCP-1/cpn60 chaperonin family / GroEL-like apical domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / in:IPR012723: / GroEL-GroES complex / 'de novo' protein folding / chaperone cofactor-dependent protein refolding / virion assembly / protein folding / response to radiation / unfolded protein binding / response to heat / protein refolding / ATPase activity / cell cycle / cell division / magnesium ion binding / membrane / ATP binding / identical protein binding / cytosol / 60 kDa chaperonin
Function and homology information
SourceEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsLudtke SJ / Baker ML / Chen D / Song J / Chuang DT / Chiu W
CitationJournal: Structure / Year: 2008
Title: De novo backbone trace of GroEL from single particle electron cryomicroscopy.
Authors: Steven J Ludtke / Matthew L Baker / Dong-Hua Chen / Jiu-Li Song / David T Chuang / Wah Chiu
Validation ReportPDB-ID: 3cau

SummaryFull reportAbout validation report
DateDeposition: Jan 25, 2008 / Header (metadata) release: Feb 12, 2008 / Map release: Apr 14, 2009 / Last update: Nov 9, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-3cau
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-3cau
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

Fileemd_5001.map.gz (map file in CCP4 format, 31251 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.06 Å/pix.
= 212. Å
200 pix
1.06 Å/pix.
= 212. Å
200 pix
1.06 Å/pix.
= 212. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.597 (by author), 0.6 (movie #1):
Minimum - Maximum-0.96591181 - 2.42435789
Average (Standard dev.)0.06689823 (0.23771034)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-100-100-100
Limit999999
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z212.000212.000212.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.9662.4240.067

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Supplemental data

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Sample components

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Entire Native unliganded GroEL, residual ADP

EntireName: Native unliganded GroEL, residual ADP / Number of components: 1 / Oligomeric State: Two back to back homo-heptameric rings
MassTheoretical: 800 kDa

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Component #1: protein, GroEL

ProteinName: GroEL / a.k.a: GroEL / Oligomeric Details: 14-mer / Recombinant expression: Yes / Number of Copies: 14
MassTheoretical: 800 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pGroESL / Strain: ESts CG-712
External referencesInterPro: InterPro: IPR012723 / Gene Ontology: protein folding

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 20 mM Tris.HCl, pH 7.5, 50 mM MgCl2
Support filmQuantifoil grids with 2 um holes
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Method: Blot for 2 sec / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: JEOL 3000SFF / Date: Jan 1, 2005 / Details: low dose on JEOL 3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 36 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 60000 X (nominal) / Cs: 1.6 mm / Imaging mode: OTHER / Defocus: 900 - 2300 nm
Specimen HolderHolder: Top entry / Model: OTHER / Temperature: 4 K ( 4 - 4 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 135 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 14

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 20401 / Applied symmetry: D7 (2*7 fold dihedral)
3D reconstructionAlgorithm: projection matching / Software: EMAN / CTF correction: per micrograph / Resolution: 4.2 Å / Resolution method: FSC 0.5

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