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- EMDB-1292: Structural basis of allosteric changes in the GroEL mutant Arg197... -

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Basic information

Entry
Database: EMDB / ID: EMD-1292
TitleStructural basis of allosteric changes in the GroEL mutant Arg197-->Ala.
Map dataR197A Mutant of GroEL with 50uM ATp
Sample
  • Sample: R197A mutant of GroEL, 50uM ATP
  • Protein or peptide: R197A mutant of GroEL
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsWhite HE / Chen S / Roseman AM / Yifrach O / Horovitz A / SAibil HR
CitationJournal: Nat Struct Biol / Year: 1997
Title: Structural basis of allosteric changes in the GroEL mutant Arg197-->Ala.
History
DepositionNov 9, 2006-
Header (metadata) releaseNov 9, 2006-
Map releaseNov 9, 2006-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019729
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.019729
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1292.gif

Downloads & links

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Map

FileDownload / File: emd_1292.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationR197A Mutant of GroEL with 50uM ATp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.6 Å/pix.
x 64 pix.
= 358.4 Å		5.6 Å/pix.
x 64 pix.
= 358.4 Å		5.6 Å/pix.
x 64 pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.6 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.00185 / Movie #1: 0.019729
Minimum - Maximum-0.0407729 - 0.0550512
Average (Standard dev.)-0.000022692 (±0.00627854)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 358.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.65.65.6
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.0410.055-0.000

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Supplemental data

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Sample components

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Entire : R197A mutant of GroEL, 50uM ATP

EntireName: R197A mutant of GroEL, 50uM ATP
Components
  • Sample: R197A mutant of GroEL, 50uM ATP
  • Protein or peptide: R197A mutant of GroEL

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Supramolecule #1000: R197A mutant of GroEL, 50uM ATP

SupramoleculeName: R197A mutant of GroEL, 50uM ATP / type: sample / ID: 1000 / Oligomeric state: 14-mer / Number unique components: 1

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Macromolecule #1: R197A mutant of GroEL

MacromoleculeName: R197A mutant of GroEL / type: protein_or_peptide / ID: 1 / Details: MUTANT / Number of copies: 1 / Oligomeric state: 14-mer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)

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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 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris, 10mM KCl, 8mmM MgCl2,50uM ATP
GridDetails: holey carbon
VitrificationCryogen name: ETHANE
Timed resolved state: Vitrified within 5 secs of ATP addition

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Electron microscopy

MicroscopeJEOL 1200EX
Image recordingCategory: FILM / Film or detector model: AGFA SCIENTA FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10 µm
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER

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Image processing

Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Software - Name: SPIDER

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Atomic model buiding 1

DetailsManual fitting in O of an apical domain of GroEL
RefinementProtocol: RIGID BODY FIT

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