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- EMDB-1677: CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase B... -

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Basic information

Entry
Database: EMDB / ID: EMD-1677
TitleCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of ATP
Map dataCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of ATP
Sample
  • Sample: Complex of Mg-chelatase subunits BchI and BchD in presence of ATP
  • Protein or peptide: Biosynthetic enzyme
KeywordsAAA+ atpase / metallation / tetrapyrroles
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 / von Willebrand factor (vWF) type A domain ...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 / von Willebrand factor (vWF) type A domain / VWFA domain profile. / 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 / Resolution: 13.0 Å
AuthorsLundqvist J / Elmlund H / Peterson-Wulff R / Elmlund D / Emanuelsson C / Hebert H / Willows R / Hansson M / Lindahl M / Al-Karadaghi S
CitationJournal: Structure / Year: 2010
Title: ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase.
Authors: Joakim Lundqvist / Hans Elmlund / Ragna Peterson Wulff / Lisa Berglund / Dominika Elmlund / Cecilia Emanuelsson / Hans Hebert / Robert D Willows / Mats Hansson / Martin Lindahl / Salam Al-Karadaghi /
Abstract: Mg-chelatase catalyzes the first committed step of the chlorophyll biosynthetic pathway, the ATP-dependent insertion of Mg(2+) into protoporphyrin IX (PPIX). Here we report the reconstruction using ...Mg-chelatase catalyzes the first committed step of the chlorophyll biosynthetic pathway, the ATP-dependent insertion of Mg(2+) into protoporphyrin IX (PPIX). Here we report the reconstruction using single-particle cryo-electron microscopy of the complex between subunits BchD and BchI of Rhodobacter capsulatus Mg-chelatase in the presence of ADP, the nonhydrolyzable ATP analog AMPPNP, and ATP at 7.5 A, 14 A, and 13 A resolution, respectively. We show that the two AAA+ modules of the subunits form a unique complex of 3 dimers related by a three-fold axis. The reconstructions demonstrate substantial differences between the conformations of the complex in the presence of ATP and ADP, and suggest that the C-terminal integrin-I domains of the BchD subunits play a central role in transmitting conformational changes of BchI to BchD. Based on these data a model for the function of magnesium chelatase is proposed.
History
DepositionJan 8, 2010-
Header (metadata) releaseJan 18, 2010-
Map releaseJan 21, 2010-
UpdateMar 13, 2013-
Current statusMar 13, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1677.jpg

Downloads & links

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Map

FileDownload / File: emd_1677.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of ATP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.33 Å/pix.
x 80 pix.
= 186.4 Å		2.33 Å/pix.
x 80 pix.
= 186.4 Å		2.33 Å/pix.
x 80 pix.
= 186.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.817642 - 1.62923
Average (Standard dev.)0.0217686 (±0.146476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-40
Dimensions808080
Spacing808080
CellA=B=C: 186.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.332.332.33
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z186.400186.400186.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-0.8181.6290.022

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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 ATP

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

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

SupramoleculeName: Complex of Mg-chelatase subunits BchI and BchD in presence of ATP
type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2010F
Image recordingDigitization - Scanner: ZEISS SCAI / Number real images: 15
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
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: 13.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 30721
Final two d classificationNumber classes: 616

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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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