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- EMDB-1734: Rubisco in complex with Rubisco large subunit methyltransferase -

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Basic information

Entry
Database: EMDB / ID: EMD-1734
TitleRubisco in complex with Rubisco large subunit methyltransferase
Map dataCryo-EM volume of RuBisCO
Sample
  • Sample: Spinach RuBisCO
  • Protein or peptide: RuBisCO
KeywordsRubisco / carbon fixation / methylation
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 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 25, 2010-
Header (metadata) releaseJul 23, 2010-
Map releaseJul 23, 2010-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.076
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.076
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1734.tif

Downloads & links

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Map

FileDownload / File: emd_1734.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM volume of RuBisCO
Voxel sizeX=Y=Z: 4.1 Å
Density
Contour LevelBy AUTHOR: 0.076 / Movie #1: 0.076
Minimum - Maximum-0.0342804 - 0.34799
Average (Standard dev.)0.000665613 (±0.0148949)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 328 Å
α=β=γ: 90 °

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-0.0340.3480.001

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Supplemental data

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Sample components

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Entire : Spinach RuBisCO

EntireName: Spinach RuBisCO
Components
  • Sample: Spinach RuBisCO
  • Protein or peptide: RuBisCO

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Supramolecule #1000: Spinach RuBisCO

SupramoleculeName: Spinach RuBisCO / type: sample / ID: 1000
Details: The sample was thawed from storage at -80 degrees Celsius before being loaded onto the grid.
Oligomeric state: Hexadecamer / Number unique components: 1
Molecular weightExperimental: 534 KDa / Theoretical: 534 KDa

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Macromolecule #1: RuBisCO

MacromoleculeName: RuBisCO / type: protein_or_peptide / ID: 1 / Name.synonym: RuBisCO / Number of copies: 1 / Oligomeric state: Hexadecamer / Recombinant expression: Yes
Source (natural)Organism: Spinacia oleracea (spinach) / synonym: Spinach / Tissue: Stroma / Cell: Plant leaves / Organelle: Chloroplast / Location in cell: Stroma
Molecular weightExperimental: 534 KDa / Theoretical: 534 KDa
Recombinant expressionOrganism: Spinacia oleracea (spinach)

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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 seconds 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: OTHER / 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: CTF correction of each particle
Final angle assignmentDetails: SPIDER:theta 45 degrees, phi 45 degrees
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX / Details: D4 symmetry applied to final reconstruction / 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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