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- EMDB-5002: Native, unliganded GroEL, C7 symmetrized, 4.7 A resolution 0.5 cr... -

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Basic information

Entry
Database: EMDB / ID: EMD-5002
TitleNative, unliganded GroEL, C7 symmetrized, 4.7 A resolution 0.5 criterion
Map dataC7 structure of unliganded apo-GroEL at 4.7 Angstrom resolution
Sample
  • Sample: Native unliganded GroEL, residual ADP
  • Protein or peptide: GroEL
Keywordsgroel / chaperonin / chaperone / backbone trace / eman / single particle
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / : / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / : / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
: / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
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 /
Abstract: In this work, we employ single-particle electron cryo-microscopy (cryo-EM) to reconstruct GroEL to approximately 4 A resolution with both D7 and C7 symmetry. Using a newly developed skeletonization ...In this work, we employ single-particle electron cryo-microscopy (cryo-EM) to reconstruct GroEL to approximately 4 A resolution with both D7 and C7 symmetry. Using a newly developed skeletonization algorithm and secondary structure element identification in combination with sequence-based secondary structure prediction, we demonstrate that it is possible to achieve a de novo Calpha trace directly from a cryo-EM reconstruction. The topology of our backbone trace is completely accurate, though subtle alterations illustrate significant differences from existing crystal structures. In the map with C7 symmetry, the seven monomers in each ring are identical; however, the subunits have a subtly different structure in each ring, particularly in the equatorial domain. These differences include an asymmetric salt bridge, density in the nucleotide-binding pocket of only one ring, and small shifts in alpha helix positions. This asymmetric conformation is different from previous asymmetric structures, including GroES-bound GroEL, and may represent a "primed state" in the chaperonin pathway.
History
DepositionJan 28, 2008-
Header (metadata) releaseFeb 12, 2008-
Map releaseApr 14, 2009-
UpdateNov 16, 2016-
Current statusNov 16, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3c9v
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3c9v
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5002_1.png

Downloads & links

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Map

FileDownload / File: emd_5002.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC7 structure of unliganded apo-GroEL at 4.7 Angstrom resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 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

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.8 / Movie #1: 0.7
Minimum - Maximum-0.74781662 - 1.95123911
Average (Standard dev.)0.04077248 (±0.20358373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z254.400254.400254.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
D min/max/mean-0.7481.9510.041

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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
Components
  • Sample: Native unliganded GroEL, residual ADP
  • Protein or peptide: GroEL

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Supramolecule #1000: Native unliganded GroEL, residual ADP

SupramoleculeName: Native unliganded GroEL, residual ADP / type: sample / ID: 1000 / Oligomeric state: Two back to back homo-heptameric rings / Number unique components: 1
Molecular weightTheoretical: 800 KDa

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Macromolecule #1: GroEL

MacromoleculeName: GroEL / type: protein_or_peptide / ID: 1 / Name.synonym: GroEL / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 800 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: ESts CG-712 / Recombinant plasmid: pGroESL
SequenceGO: protein folding / InterPro: INTERPRO: IPR012723

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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

BufferDetails: 20 mM Tris.HCl, pH 7.5, 50 mM MgCl2
GridDetails: Quantifoil grids with 2 um holes
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 2 sec

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Electron microscopy

MicroscopeJEOL 3000SFF
TemperatureMin: 4 K / Max: 4 K / Average: 4 K
Detailslow dose on JEOL 3000SFF
DateJan 1, 2005
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 135 / Average electron dose: 36 e/Å2 / Bits/pixel: 14
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 1.6 mm / Nominal defocus max: 2.3 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Top entry / Specimen holder model: OTHER

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Image processing

CTF correctionDetails: per micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 20401

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