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- EMDB-3701: Structure of Rubisco from Rhodobacter sphaeroides in complex with... -

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Basic information

Entry
Database: EMDB / ID: 3701
TitleStructure of Rubisco from Rhodobacter sphaeroides in complex with CABP and RcaCC
SampleRubisco-RcaCC complex
SourceRhodobacter sphaeroides / archaea / ロドバクター・スファエロイデス
Map data
Methodsingle particle reconstruction, at 7.56 Å resolution
AuthorsBracher A / Milicic G / Ciniawsky S / Wendler P / Hayer-Hartl M / Hartl FU
CitationMol. Cell, 2017

Mol. Cell, 2017 StrPapers
Mechanism of Enzyme Repair by the AAA(+) Chaperone Rubisco Activase.
Javaid Y Bhat / Goran Miličić / Gabriel Thieulin-Pardo / Andreas Bracher / Andrew Maxwell / Susanne Ciniawsky / Oliver Mueller-Cajar / John R Engen / F Ulrich Hartl / Petra Wendler / Manajit Hayer-Hartl

DateDeposition: May 3, 2017 / Header (metadata) release: May 10, 2017 / Map release: Jul 26, 2017 / Last update: Jul 26, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0527
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0527
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3701.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.04 Å/pix.
= 332.8 Å
320 pix
1.04 Å/pix.
= 332.8 Å
320 pix
1.04 Å/pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour Level:0.0527 (by author), 0.0527 (movie #1):
Minimum - Maximum-0.12483833 - 0.18102548
Average (Standard dev.)0.002020328 (0.012549733)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1250.1810.002

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Supplemental data

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Sample components

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Entire Rubisco-RcaCC complex

EntireName: Rubisco-RcaCC complex
Details: Rubisco was treated with the inhibitor CABP. RcaCC, ATP, ATP-gammaS and RuBP were added. The sample was treated with glutaraldehyde crosslinker. Rubisco-RcaCC complexes were purified by SEC.
Number of components: 4
MassExperimental: 768 kDa

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Component #1: protein, Rubisco-RcaCC complex

ProteinName: Rubisco-RcaCC complex
Details: Rubisco was treated with the inhibitor CABP. RcaCC, ATP, ATP-gammaS and RuBP were added. The sample was treated with glutaraldehyde crosslinker. Rubisco-RcaCC complexes were purified by SEC.
Recombinant expression: No
MassExperimental: 768 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

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Component #2: protein, CbbX

ProteinName: CbbX / Recombinant expression: No
Source (engineered)Expression System: Rhodobacter sphaeroides / archaea / ロドバクター・スファエロイデス

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Component #3: protein, RbcL

ProteinName: RbcL / Recombinant expression: No
Source (engineered)Expression System: Rhodobacter sphaeroides / archaea / ロドバクター・スファエロイデス

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Component #4: protein, RbcS

ProteinName: RbcS / Recombinant expression: No
Source (engineered)Expression System: Rhodobacter sphaeroides / archaea / ロドバクター・スファエロイデス

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.3 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: Cs corrected Krios 1 at NeCEN (June 2016)
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 333711
3D reconstructionSoftware: RELION / Resolution: 7.56 Å / Resolution method: FSC 0.143 CUT-OFF

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