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- EMDB-1735: Rubisco in complex with Rubisco large subunit methyltransferase -

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Basic information

Entry
Database: EMDB / ID: EMD-1735
TitleRubisco in complex with Rubisco large subunit methyltransferase
Map dataThis is a volume of RuBisCO in complex with RuBisCO large subunit methyl transferase
Sample
  • Sample: Spinach RuBisCO in complex with pea RuBisCO LSMT
  • Protein or peptide: Ribulose-1,5-bisphosphate carboxylase oxygenase
  • Protein or peptide: RuBisCO large subunit methyl transferase
KeywordsRubisco / carbon fixation / methylation
Biological speciesSpinacia oleracea (spinach) / Pisum sativum (garden pea)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsRaunser S / Magnani R / Huang Z / Houtz RL / Trievel RC / Penczek PA / Walz T
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: Rubisco in complex with Rubisco large subunit methyltransferase.
Authors: Stefan Raunser / Roberta Magnani / Zhong Huang / Robert L Houtz / Raymond C Trievel / Pawel A Penczek / Thomas Walz /
Abstract: SET domain protein lysine methyltransferases (PKMT) are a structurally unique class of enzymes that catalyze the specific methylation of lysine residues in a number of different substrates. ...SET domain protein lysine methyltransferases (PKMT) are a structurally unique class of enzymes that catalyze the specific methylation of lysine residues in a number of different substrates. Especially histone-specific SET domain PKMTs have received widespread attention because of their roles in the regulation of epigenetic gene expression and the development of some cancers. Rubisco large subunit methyltransferase (RLSMT) is a chloroplast-localized SET domain PKMT responsible for the formation of trimethyl-lysine-14 in the large subunit of Rubisco, an essential photosynthetic enzyme. Here, we have used cryoelectron microscopy to produce an 11-A density map of the Rubisco-RLSMT complex. The atomic model of the complex, obtained by fitting crystal structures of Rubisco and RLSMT into the density map, shows that the extensive contact regions between the 2 proteins are mainly mediated by hydrophobic residues and leucine-rich repeats. It further provides insights into potential conformational changes that may occur during substrate binding and catalysis. This study presents the first structural analysis of a SET domain PKMT in complex with its intact polypeptide substrate.
History
DepositionMay 26, 2010-
Header (metadata) releaseJul 23, 2010-
Map releaseJul 23, 2010-
UpdateMay 16, 2012-
Current statusMay 16, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1735.tif

Downloads & links

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Map

FileDownload / File: emd_1735.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a volume of RuBisCO in complex with RuBisCO large subunit methyl transferase
Voxel sizeX=Y=Z: 4.1 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.09922165 - 1.71805418
Average (Standard dev.)0.00282996 (±0.01885465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-100
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.0991.7180.003

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Supplemental data

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Sample components

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Entire : Spinach RuBisCO in complex with pea RuBisCO LSMT

EntireName: Spinach RuBisCO in complex with pea RuBisCO LSMT
Components
  • Sample: Spinach RuBisCO in complex with pea RuBisCO LSMT
  • Protein or peptide: Ribulose-1,5-bisphosphate carboxylase oxygenase
  • Protein or peptide: RuBisCO large subunit methyl transferase

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Supramolecule #1000: Spinach RuBisCO in complex with pea RuBisCO LSMT

SupramoleculeName: Spinach RuBisCO in complex with pea RuBisCO LSMT / type: sample / ID: 1000
Details: The sample was thawed from storage at -80 degrees Celcius before being loaded onto the grid.
Oligomeric state: One monomer of LSMT binds to a RuBisCO hexadecamer
Number unique components: 2
Molecular weightExperimental: 585 KDa / Theoretical: 585 KDa

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Macromolecule #1: Ribulose-1,5-bisphosphate carboxylase oxygenase

MacromoleculeName: Ribulose-1,5-bisphosphate carboxylase oxygenase / type: protein_or_peptide / ID: 1 / Name.synonym: RuBisCO / Number of copies: 1 / Oligomeric state: Hexadecamer / Recombinant expression: No
Source (natural)Organism: Spinacia oleracea (spinach) / synonym: Spinach / Tissue: Plant leaves / Organelle: Chloroplast / Location in cell: Stroma
Molecular weightExperimental: 534 KDa / Theoretical: 534 KDa

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Macromolecule #2: RuBisCO large subunit methyl transferase

MacromoleculeName: RuBisCO large subunit methyl transferase / type: protein_or_peptide / ID: 2 / Name.synonym: RLSMT / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Pisum sativum (garden pea) / synonym: Pea / Tissue: Plant leaves / Organelle: Chloroplast / Location in cell: Stroma
Molecular weightExperimental: 55 KDa / Theoretical: 55 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pDEST14

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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

Concentration5 mg/mL
BufferpH: 8 / Details: 50 mM Tris-HCl pH 8, 5 mM MgCl2, 1 mM EDTA
GridDetails: Quantifoil grids 2 um holes
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 1 s before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51159 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder.
Specimen holder model: OTHER
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 110 / Average electron dose: 15 e/Å2
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final angle assignmentDetails: SPIDER:theta 45 degrees, phi 45 degrees
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX / Number images used: 29000
DetailsThe particles were selected interactively at the computer terminal.

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Atomic model buiding 1

Initial modelPDB ID:

1rxo

SoftwareName: SITUS
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor

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Atomic model buiding 2

Initial modelPDB ID:

1mlv

SoftwareName: SITUS
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor

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