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- EMDB-1080: A 11.5 A single particle reconstruction of GroEL using EMAN. -

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Basic information

Entry
Database: EMDB / ID: EMD-1080
TitleA 11.5 A single particle reconstruction of GroEL using EMAN.
Map dataThis is the volumetric data for our published 11.5 A resolution reconstruction of GroEL. Note that newer EMAN releases can refine the same data to ~9 A resolution.
Sample
  • Sample: native naked GroEL
  • Protein or peptide: GroEL
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsLudtke SJ / Jakana J / Song J / Chuang DT / Chiu W
CitationJournal: J Mol Biol / Year: 2001
Title: A 11.5 A single particle reconstruction of GroEL using EMAN.
Authors: S J Ludtke / J Jakana / J L Song / D T Chuang / W Chiu /
Abstract: Single-particle analysis has become an increasingly important method for structural determination of large macromolecular assemblies. GroEL is an 800 kDa molecular chaperone, which, along with its co- ...Single-particle analysis has become an increasingly important method for structural determination of large macromolecular assemblies. GroEL is an 800 kDa molecular chaperone, which, along with its co-chaperonin GroES, promotes protein folding both in vitro and in the bacterial cell. EMAN is a single-particle analysis software package, which was first publicly distributed in 2000. We present a three-dimensional reconstruction of native naked GroEL to approximately 11.5 A performed entirely with EMAN. We demonstrate that the single-particle reconstruction, X-ray scattering data and X-ray crystal structure all agree well at this resolution. These results validate the specific methods of image restoration, reconstruction and evaluation techniques implemented in EMAN. It also demonstrates that the single-particle reconstruction technique and X-ray crystallography will yield consistent structure factors, even at low resolution, when image restoration is performed correctly. A detailed comparison of the single-particle and X-ray structures exhibits some small variations in the equatorial domain of the molecule, likely due to the absence of crystal packing forces in the single-particle reconstruction.
History
DepositionMay 6, 2004-
Header (metadata) releaseMay 12, 2004-
Map releaseMay 12, 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: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1oel
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1080.gif

Downloads & links

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Map

FileDownload / File: emd_1080.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the volumetric data for our published 11.5 A resolution reconstruction of GroEL. Note that newer EMAN releases can refine the same data to ~9 A resolution.
Voxel sizeX=Y=Z: 2.7 Å
Density
Contour Level1: 0.852 / Movie #1: 1
Minimum - Maximum-1.34116 - 2.36503
Average (Standard dev.)0.0813288 (±0.324536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 267.3 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z999999
origin x/y/z0.0000.0000.000
length x/y/z267.300267.300267.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-20-59
NX/NY/NZ181231119
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-1.3412.3650.081

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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: 14-mer / 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 4000EX
Electron beamAcceleration voltage: 400 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.1 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 5 / Average electron dose: 30 e/Å2
Details: Data was median filtered to 14 microns/pixel after scanning.
Bits/pixel: 8

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Image processing

CTF correctionDetails: Per particle phase flipping, amplitude correction during averaging
Final two d classificationNumber classes: 334
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 4916
DetailsNote that class averages are EMAN-style reference-based, not MSA.

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Atomic model buiding 1

Initial modelPDB ID:

1oel

SoftwareName: foldhunter EMAN
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient

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