+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1734 | |||||||||
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Title | Rubisco in complex with Rubisco large subunit methyltransferase | |||||||||
Map data | Cryo-EM volume of RuBisCO | |||||||||
Sample |
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Keywords | Rubisco / carbon fixation / methylation | |||||||||
Biological species | Spinacia oleracea (spinach) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Raunser S / Magnani R / Huang Z / Houtz RL / Trievel RC / Penczek PA / Walz T | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1734.map.gz | 1.9 MB | EMDB map data format | |
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Header (meta data) | emd-1734-v30.xml emd-1734.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | EMD-1734.tif | 763.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1734 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1734 | HTTPS FTP |
-Validation report
Summary document | emd_1734_validation.pdf.gz | 229.3 KB | Display | EMDB validaton report |
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Full document | emd_1734_full_validation.pdf.gz | 228.4 KB | Display | |
Data in XML | emd_1734_validation.xml.gz | 4.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1734 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1734 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1734.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM volume of RuBisCO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Spinach RuBisCO
Entire | Name: Spinach RuBisCO |
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Components |
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-Supramolecule #1000: Spinach RuBisCO
Supramolecule | Name: 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 |
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Molecular weight | Experimental: 534 KDa / Theoretical: 534 KDa |
-Macromolecule #1: RuBisCO
Macromolecule | Name: RuBisCO / type: protein_or_peptide / ID: 1 / Name.synonym: RuBisCO / Number of copies: 1 / Oligomeric state: Hexadecamer / Recombinant expression: Yes |
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Source (natural) | Organism: Spinacia oleracea (spinach) / synonym: Spinach / Tissue: Stroma / Cell: Plant leaves / Organelle: Chloroplast / Location in cell: Stroma |
Molecular weight | Experimental: 534 KDa / Theoretical: 534 KDa |
Recombinant expression | Organism: Spinacia oleracea (spinach) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 8 / Details: 50 mM Tris-HCl pH 8, 5 mM MgCl2, 1 mM EDTA |
Grid | Details: Quantifoil grids 2 um holes |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 1 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Category: 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 min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 51159 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder. Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected interactively at the computer terminal. |
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CTF correction | Details: CTF correction of each particle |
Final reconstruction | Applied 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 |
Final angle assignment | Details: SPIDER:theta 45 degrees, phi 45 degrees |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: SITUS |
Details | Protocol: Rigid Body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor |