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- EMDB-1081: Seeing GroEL at 6 A resolution by single particle electron cryomi... -

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Basic information

Entry
Database: EMDB / ID: EMD-1081
TitleSeeing GroEL at 6 A resolution by single particle electron cryomicroscopy.
Map dataThis is the density map for the final published ~6 A resolution GroEL structure.
Sample
  • Sample: native naked GroEL
  • Protein or peptide: GroEL
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsLudtke SJ / Chen D / Song J / Chuang DT / Chiu W
CitationJournal: Structure / Year: 2004
Title: Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy.
Authors: Steven J Ludtke / Dong-Hua Chen / Jiu-Li Song / David T Chuang / Wah Chiu /
Abstract: We present a reconstruction of native GroEL by electron cryomicroscopy (cryo-EM) and single particle analysis at 6 A resolution. alpha helices are clearly visible and beta sheet density is also ...We present a reconstruction of native GroEL by electron cryomicroscopy (cryo-EM) and single particle analysis at 6 A resolution. alpha helices are clearly visible and beta sheet density is also visible at this resolution. While the overall conformation of this structure is quite consistent with the published X-ray data, a measurable shift in the positions of three alpha helices in the intermediate domain is observed, not consistent with any of the 7 monomeric structures in the Protein Data Bank model (1OEL). In addition, there is evidence for slight rearrangement or flexibility in parts of the apical domain. The 6 A resolution cryo-EM GroEL structure clearly demonstrates the veracity and expanding scope of cryo-EM and the single particle reconstruction technique for macromolecular machines.
History
DepositionMay 13, 2004-
Header (metadata) releaseMay 14, 2004-
Map releaseJul 14, 2004-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.457584446
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.457584446
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-1oel
  • Surface level: 0.457584446
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-1oel
  • Surface level: 0.457584446
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1081.gif

Downloads & links

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Map

FileDownload / File: emd_1081.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the density map for the final published ~6 A resolution GroEL structure.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.08 Å/pix.
x 128 pix.
= 264.16 Å		2.08 Å/pix.
x 128 pix.
= 264.16 Å		2.08 Å/pix.
x 128 pix.
= 264.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.08 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.209 / Movie #1: 0.4575844
Minimum - Maximum-1.19262 - 1.78203
Average (Standard dev.)-0.000000000096827 (±0.148809)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 264.16 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.082.082.08
M x/y/z127127127
origin x/y/z0.0000.0000.000
length x/y/z264.160264.160264.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-20-59
NX/NY/NZ181231119
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-1.1931.782-0.000

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Supplemental data

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Sample components

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Entire : native naked GroEL

EntireName: native naked GroEL
Components
  • Sample: native naked GroEL
  • Protein or peptide: GroEL

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Supramolecule #1000: native naked GroEL

SupramoleculeName: native naked GroEL / type: sample / ID: 1000 / Oligomeric state: homo 14-mer / Number unique components: 1
Molecular weightTheoretical: 800 KDa

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Macromolecule #1: GroEL

MacromoleculeName: GroEL / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Oligomeric state: 14mer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightExperimental: 57 KDa
Recombinant expressionOrganism: ESts CG-712 / Recombinant plasmid: pGroESL

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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 / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Manual gravity plunger

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Electron microscopy

MicroscopeJEOL 2010F
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 42 / Average electron dose: 18 e/Å2
Details: Data was median filtered to 10.5 microns/pixel after scanning.
Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.0 mm / Nominal defocus max: 2.56 µm / Nominal defocus min: 0.794 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsNote that class averages are EMAN-style reference-based, not MSA.
CTF correctionDetails: per-particle phase flipping pre-processing, amplitude correction during class averaging
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 39085
Final two d classificationNumber classes: 295

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Atomic model buiding 1

Initial modelPDB ID:

1oel

SoftwareName: foldhunter, EMAN
DetailsProtocol: Rigid Body. rigid body fitting of 1 monomer from 1OEL initially, followed by rigid body refinement of each domain, apical, intermediate and equatorial.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient

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