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- EMDB-1654: Rubisco RbcL8-RbcX2-8 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-1654
TitleRubisco RbcL8-RbcX2-8 complex
Map dataThis is a negative stain 3D reconstruction of a Rubisco assembly intermediate comprising eight copies of the large subunit RbcL and eight copies of the assembly chaperone RbcX2.
Sample
  • Sample: RbcL8-X8 Rubisco assembly intermediate containing 8 copies of the large Rubisco subunit RbcL and eight copies of the dimeric assembly chaperone RbcX2.
  • Protein or peptide: RbcL
  • Protein or peptide: RbcX
KeywordsPhotosynthesis / protein folding / Rubisco / Rubisco assembly / chaperones
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / reductive pentose-phosphate cycle / photosynthesis / protein folding chaperone / monooxygenase activity ...ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / reductive pentose-phosphate cycle / photosynthesis / protein folding chaperone / monooxygenase activity / magnesium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
RuBisCO chaperone RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal ...RuBisCO chaperone RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain / RuBisCO chaperone RbcX
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria) / Anabaena sp. (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 Å
AuthorsLiu C / Young AL / Starling-Windhof A / Bracher A / Saschenbrecker S / Rao BV / Berninghausen O / Mielke T / Hartl FU / Beckmann R / Hayer-Hartl M
CitationJournal: Nature / Year: 2010
Title: Coupled chaperone action in folding and assembly of hexadecameric Rubisco.
Authors: Cuimin Liu / Anna L Young / Amanda Starling-Windhof / Andreas Bracher / Sandra Saschenbrecker / Bharathi Vasudeva Rao / Karnam Vasudeva Rao / Otto Berninghausen / Thorsten Mielke / F Ulrich ...Authors: Cuimin Liu / Anna L Young / Amanda Starling-Windhof / Andreas Bracher / Sandra Saschenbrecker / Bharathi Vasudeva Rao / Karnam Vasudeva Rao / Otto Berninghausen / Thorsten Mielke / F Ulrich Hartl / Roland Beckmann / Manajit Hayer-Hartl /
Abstract: Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The ...Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The limited catalytic efficiency of Rubisco has sparked extensive efforts to re-engineer the enzyme with the goal of enhancing agricultural productivity. To facilitate such efforts we analysed the formation of cyanobacterial form I Rubisco by in vitro reconstitution and cryo-electron microscopy. We show that RbcL subunit folding by the GroEL/GroES chaperonin is tightly coupled with assembly mediated by the chaperone RbcX(2). RbcL monomers remain partially unstable and retain high affinity for GroEL until captured by RbcX(2). As revealed by the structure of a RbcL(8)-(RbcX(2))(8) assembly intermediate, RbcX(2) acts as a molecular staple in stabilizing the RbcL subunits as dimers and facilitates RbcL(8) core assembly. Finally, addition of RbcS results in RbcX(2) release and holoenzyme formation. Specific assembly chaperones may be required more generally in the formation of complex oligomeric structures when folding is closely coupled to assembly.
History
DepositionOct 20, 2009-
Header (metadata) releaseOct 27, 2009-
Map releaseJan 20, 2010-
UpdateJan 20, 2010-
Current statusJan 20, 2010Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2wvw
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1654.gif

emd_1654.jpg

Downloads & links

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Map

FileDownload / File: emd_1654.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a negative stain 3D reconstruction of a Rubisco assembly intermediate comprising eight copies of the large subunit RbcL and eight copies of the assembly chaperone RbcX2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.31 Å/pix.
x 112 pix.
= 370.496 Å		3.31 Å/pix.
x 112 pix.
= 370.496 Å		3.31 Å/pix.
x 112 pix.
= 370.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.308 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-19.867999999999999 - 12.818
Average (Standard dev.)0.000000000998943 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-56-56-56
Dimensions112112112
Spacing112112112
CellA=B=C: 370.496 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.3083.3083.308
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z370.496370.496370.496
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-56-56-56
NC/NR/NS112112112
D min/max/mean-19.86812.8180.000

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Supplemental data

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Sample components

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Entire : RbcL8-X8 Rubisco assembly intermediate containing 8 copies of the...

EntireName: RbcL8-X8 Rubisco assembly intermediate containing 8 copies of the large Rubisco subunit RbcL and eight copies of the dimeric assembly chaperone RbcX2.
Components
  • Sample: RbcL8-X8 Rubisco assembly intermediate containing 8 copies of the large Rubisco subunit RbcL and eight copies of the dimeric assembly chaperone RbcX2.
  • Protein or peptide: RbcL
  • Protein or peptide: RbcX

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Supramolecule #1000: RbcL8-X8 Rubisco assembly intermediate containing 8 copies of the...

SupramoleculeName: RbcL8-X8 Rubisco assembly intermediate containing 8 copies of the large Rubisco subunit RbcL and eight copies of the dimeric assembly chaperone RbcX2.
type: sample / ID: 1000
Oligomeric state: one RbcL-octamer binds to on RbcX2 octamer
Number unique components: 2
Molecular weightTheoretical: 660 KDa

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Macromolecule #1: RbcL

MacromoleculeName: RbcL / type: protein_or_peptide / ID: 1 / Name.synonym: Rubisco large subunit / Number of copies: 8 / Oligomeric state: Octamer / Recombinant expression: Yes
Source (natural)Organism: Synechococcus elongatus (bacteria) / Strain: PCC 6301
Molecular weightTheoretical: 52.5 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant plasmid: pet11a

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Macromolecule #2: RbcX

MacromoleculeName: RbcX / type: protein_or_peptide / ID: 2 / Name.synonym: RbcX / Number of copies: 16 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Anabaena sp. (bacteria)
Molecular weightTheoretical: 30.4 KDa
Recombinant expressionOrganism: Eschericia coli BL21(DE3) / Recombinant plasmid: pet28b

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.7 / Details: 20 mM Tris-HCl, pH 8.7
StainingType: NEGATIVE / Details: Uranyl acetate
GridDetails: Quantifoil grids (3/3) with 2 nm carbon on top
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
TemperatureAverage: 293 K
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (2k x 2k) / Digitization - Sampling interval: 3.308 µm / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 90000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 90000
Sample stageSpecimen holder: Single tilt tomography holder / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1 / Number images used: 2809
Final angle assignmentDetails: EMAN1

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Atomic model buiding 1

Initial modelPDB ID:

3hyb

SoftwareName: chimera
DetailsProtocol: rigid body. rigid body fitting using UCSF Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2wvw:
Cryo-EM structure of the RbcL-RbcX complex

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