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- EMDB-1656: Control structure of the RbcL8 octamer -

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Basic information

Entry
Database: EMDB / ID: EMD-1656
TitleControl structure of the RbcL8 octamer
Map dataThis is cryo-EM map of the rubisco large subunit octamer
Sample
  • Sample: Rubisco large subnuit octamer
  • Protein or peptide: RbcL
Keywordsphotosynthesis / protein folding / Rubisco / Rubisco assembly / chaperones
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone / photosynthesis / monooxygenase activity ...ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone / photosynthesis / 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)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 16.0 Å
AuthorsLiu C / Young A / Starling-Windhof A / Bracher A / Saschenbrecker S / Rao BV / Rao KV / Berninghausen O / Mielke T / Hartl FU ...Liu C / Young A / Starling-Windhof A / Bracher A / Saschenbrecker S / Rao BV / Rao KV / 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: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2wvw
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1656.jpg

Downloads & links

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Map

FileDownload / File: emd_1656.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is cryo-EM map of the rubisco large subunit octamer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.3 Å/pix.
x 112 pix.
= 369.6 Å		3.3 Å/pix.
x 112 pix.
= 369.6 Å		3.3 Å/pix.
x 112 pix.
= 369.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 5.0 / Movie #1: 5
Minimum - Maximum-6.2346 - 10.126200000000001
Average (Standard dev.)0.00000000810747 (±0.918251)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-56-56-56
Dimensions112112112
Spacing112112112
CellA=B=C: 369.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.33.33.3
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z369.600369.600369.600
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-6.23510.1260.000

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Supplemental data

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Sample components

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Entire : Rubisco large subnuit octamer

EntireName: Rubisco large subnuit octamer
Components
  • Sample: Rubisco large subnuit octamer
  • Protein or peptide: RbcL

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Supramolecule #1000: Rubisco large subnuit octamer

SupramoleculeName: Rubisco large subnuit octamer / type: sample / ID: 1000 / Oligomeric state: Octamer / Number unique components: 1
Molecular weightTheoretical: 420 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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Experimental details

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Structure determination

Methodnegative staining, cryo EM
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: cryo-EM
GridDetails: Quantifoil grids (3/3) with 2 nm carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 85 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot
Method: 10 second blotting before plunging, used 2 layers of filter paper

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 90000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 90000
Sample stageSpecimen holder: single tilt cryo holder / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 95 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 / Details: Data collected on CCD / Bits/pixel: 16
Tilt angle max0

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Image processing

CTF correctionDetails: Each particle
Final angle assignmentDetails: EMAN
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1 / Number images used: 13217

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