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- EMDB-1676: CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase B... -

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Basic information

Entry
Database: EMDB / ID: EMD-1676
TitleCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of ADP
Map dataThis is the volume of the complex of Magnesium Chelatase subunit BchI and BchD incubated with ADP.
Sample
  • Sample: Complex of Mg-chelatase subunits BchI and BchD in presence of ADP
  • Protein or peptide: Biosynthetic enzyme
KeywordsAAA+ atpase / metallation / tetrapyrroles / Mg chelatase
Function / homology
Function and homology information


bacteriochlorophyll biosynthetic process / magnesium chelatase / magnesium chelatase activity / photosynthesis / ATP hydrolysis activity / ATP binding
Similarity search - Function
Magnesium chelatase, ATPase subunit D / Magnesium-chelatase BchD/ChlD, VWA domain / Magnesium chelatase, ATPase subunit I / ChlI/MoxR, AAA lid domain / AAA lid domain / Magnesium-chelatase subunit ChlI-like / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / von Willebrand factor type A domain / VWFA domain profile. ...Magnesium chelatase, ATPase subunit D / Magnesium-chelatase BchD/ChlD, VWA domain / Magnesium chelatase, ATPase subunit I / ChlI/MoxR, AAA lid domain / AAA lid domain / Magnesium-chelatase subunit ChlI-like / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Magnesium-chelatase 60 kDa subunit / Magnesium-chelatase 38 kDa subunit
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 7.5 Å
AuthorsLundqvist J / Elmlund H / Peterson-Wulff R / Elmlund D / Emanuelsson C / Hebert H / Willows R / Hansson M / Lindahl M / Al-Karadaghi S
CitationJournal: J Mol Biol / Year: 2008
Title: A new cryo-EM single-particle ab initio reconstruction method visualizes secondary structure elements in an ATP-fueled AAA+ motor.
Authors: Hans Elmlund / Joakim Lundqvist / Salam Al-Karadaghi / Mats Hansson / Hans Hebert / Martin Lindahl /
Abstract: The generation of ab initio three-dimensional (3D) models is a bottleneck in the studies of large macromolecular assemblies by single-particle cryo-electron microscopy. We describe here a novel ...The generation of ab initio three-dimensional (3D) models is a bottleneck in the studies of large macromolecular assemblies by single-particle cryo-electron microscopy. We describe here a novel method, in which established methods for two-dimensional image processing are combined with newly developed programs for joint rotational 3D alignment of a large number of class averages (RAD) and calculation of 3D volumes from aligned projections (VolRec). We demonstrate the power of the method by reconstructing an approximately 660-kDa ATP-fueled AAA+ motor to 7.5 A resolution, with secondary structure elements identified throughout the structure. We propose the method as a generally applicable automated strategy to obtain 3D reconstructions from unstained single particles imaged in vitreous ice.
History
DepositionJan 8, 2010-
Header (metadata) releaseJan 18, 2010-
Map releaseJan 21, 2010-
UpdateJul 3, 2013-
Current statusJul 3, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2x31
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1676.jpg

Downloads & links

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Map

FileDownload / File: emd_1676.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the volume of the complex of Magnesium Chelatase subunit BchI and BchD incubated with ADP.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 160 pix.
= 186.72 Å		1.17 Å/pix.
x 160 pix.
= 186.72 Å		1.17 Å/pix.
x 160 pix.
= 186.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.167 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.0475533 - 0.135485
Average (Standard dev.)0.00109676 (±0.00760868)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 186.72 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1671.1671.167
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z186.720186.720186.720
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0480.1350.001

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Supplemental data

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Sample components

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Entire : Complex of Mg-chelatase subunits BchI and BchD in presence of ADP

EntireName: Complex of Mg-chelatase subunits BchI and BchD in presence of ADP
Components
  • Sample: Complex of Mg-chelatase subunits BchI and BchD in presence of ADP
  • Protein or peptide: Biosynthetic enzyme

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Supramolecule #1000: Complex of Mg-chelatase subunits BchI and BchD in presence of ADP

SupramoleculeName: Complex of Mg-chelatase subunits BchI and BchD in presence of ADP
type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 660 KDa / Theoretical: 660 KDa

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Macromolecule #1: Biosynthetic enzyme

MacromoleculeName: Biosynthetic enzyme / type: protein_or_peptide / ID: 1 / Name.synonym: Mg chelatase / Recombinant expression: Yes
Source (natural)Organism: Rhodobacter capsulatus (bacteria)
Molecular weightTheoretical: 660 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration0.1 mg/mL
BufferpH: 8
StainingType: NEGATIVE / Details: Vitrification
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2010F
Image recordingDigitization - Scanner: ZEISS SCAI / Number real images: 18
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Eucentric / Specimen holder model: JEOL

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 29400
Final two d classificationNumber classes: 258

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Atomic model buiding 1

Initial modelPDB ID:

1g8p

RefinementSpace: REAL
Output model

PDB-2x31:
Modelling of the complex between subunits BchI and BchD of magnesium chelatase based on single-particle cryo-EM reconstruction at 7.5 ang

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