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- EMDB-1932: Negative stain EM Map of the AAA protein CbbX, a red-type Rubisco... -

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Basic information

Entry
Database: EMDB / ID: 1932
TitleNegative stain EM Map of the AAA protein CbbX, a red-type Rubisco activase from R. sphaeroides
KeywordsAAA+ protein / ATPase / Rubisco activase
SampleR. sphaeroides CbbX 3D density map.
SourceRhodobacter sphaeroides / archaea / ロドバクター・スファエロイデス
Map dataNegative stain EM reconstruction of the R. sphaeroides CbbX hexamer
Methodsingle particle reconstruction, at 21 A resolution
AuthorsMueller-Cajar O / Stotz M / Wendler P / Hartl FU / Bracher A / Hayer-Hartl M
CitationNature, 2011, 479, 194-199

Nature, 2011, 479, 194-199 StrPapers
Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase.
Oliver Mueller-Cajar / Mathias Stotz / Petra Wendler / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl

DateDeposition: Jul 18, 2011 / Header (metadata) release: Aug 26, 2011 / Map release: Nov 3, 2011 / Last update: Jul 18, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3zuh
  • Surface level: 0.017
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1932.map.gz (map file in CCP4 format, 8193 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
3.31 A/pix
= 423.68 A
128 pix
3.31 A/pix
= 423.68 A
128 pix
3.31 A/pix
= 423.68 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.31 A
Density
Contour Level:0.005 (by emdb), 0.017 (movie #1):
Minimum - Maximum-0.011328 - 0.197363
Average (Standard dev.)0.000343572 (0.00533179)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
CellA=B=C: 423.68 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z3.313.313.31
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z423.680423.680423.680
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0110.1970.000

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Supplemental data

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Sample components

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Entire R. sphaeroides CbbX 3D density map.

EntireName: R. sphaeroides CbbX 3D density map. / Number of components: 1 / Oligomeric State: Hexamer
MassTheoretical: 206 kDa

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Component #1: protein, Rubisco Activase

ProteinName: Rubisco Activase / a.k.a: CbbX / Oligomeric Details: Hexamer
Details: The protein is bound to Ribulose-1,5-bisphosphate, ATP and ATPgammaS
Recombinant expression: Yes / Number of Copies: 6
MassTheoretical: 206 kDa
SourceSpecies: Rhodobacter sphaeroides / archaea / ロドバクター・スファエロイデス
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli
Vector: pHue
External referencesGene Ontology: GO: 0005524

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.072 mg/ml
Buffer solution: 20 mM Tris pH 8.0, 50 mM NaCl, 5mM MgCl2, 1mM Ribulose-1,5-bisphosphate, 1mM ATP/ATPgammaS
pH: 8
Support filmplain carbon grid
StainingGrids with adsorbed protein stained with 2% (w/v) uranyl acetate for 40 seconds.
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Nov 19, 2010
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 90600 X (nominal), 90600 X (calibrated)
Astigmatism: objective lens astigmatism was corrected for at 110k magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 260 - 1800 nm
Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC
CameraDetector: FEI EAGLE (2k x 2k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 245 / Applied symmetry: C6 (6 fold cyclic)
3D reconstructionAlgorithm: angular reconstitution / Software: MRC, IMAGIC, SPIDER / CTF correction: phase flipping, each particle / Resolution: 21 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: rigid body
Input PDB model: 3SYL
Modeling #2Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: rigid body
Input PDB model: 3CF3
Output model

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