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CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP

by single particle reconstruction, at 14 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.005, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.005, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1678
TitleCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP
MapCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP
SampleComplex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP
KeywordsAAA+ atpase, metallation, tetrapyrroles
AuthorsLundqvist J, Elmlund H, Peterson-Wulff R, Elmlund D, Emanuelsson C, Hebert H, Willows R, Hansson M, Lindahl M, Al-Karadaghi S
DateDeposition: 2010-01-08, Header release: 2010-01-18, Map release: 2010-01-21, Last update: 2013-03-13
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.005, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.005, Image by UCSF CHIMERA

Supplemental images
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Related Structure Data
Related Entries

PDB-2x31

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Article
Citation - Primary
ArticleStructure, Vol. 18, Issue 3, Page 354-65, Year 2010
TitleATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase.
AuthorsJoakim Lundqvist, Hans Elmlund, Ragna Peterson Wulff, Lisa Berglund, Dominika Elmlund, Cecilia Emanuelsson, Hans Hebert, Robert D Willows, Mats Hansson, Martin Lindahl, Salam Al-Karadaghi
Department of Molecular Biophysics, Centre for Molecular Protein Science, Lund University, Lund, Sweden.
KeywordsAdenosine Triphosphate (chemistry), Amino Acid Sequence, Bacterial Proteins (chemistry), Cryoelectron Microscopy, Genes, Bacterial, Lyases (chemistry, 4.-), Models, Molecular, Molecular Sequence Data, Protein Conformation, Rhodobacter capsulatus (metabolism), magnesium chelatase (4.99.1-)
LinksPII: S0969-2126(10)00031-6, DOI: 10.1016/j.str.2010.01.001, PubMed: 20223218
Map
Fileemd_1678.map.gz ( map file in CCP4 format, 2001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
2.33 A/pix
= 186.4 A
80 pix
2.33 A/pix
= 186.4 A
80 pix
2.33 A/pix
= 186.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.005 (by author), 0.005 (movie #1):
Minimum - Maximum: -0.0280966 - 0.0773895
Average (Standard dev.): 0.000822421 (0.00452024)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin-40-40-40
Limit393939
Spacing808080
Unit CellA= B= C: 186.4 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.33 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0280.0770.001
Annotation DetailsCryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP
Supplement
Images
Images
Sample
NameComplex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP
Number of Components1
Theoretical Mass0.66MDa
Component #1: protein - Mg chelatase
Scientific nameBiosynthetic enzyme
Common NameMg chelatase
Theoretical Mass0.66 MDa
Scientific Name of SpeciesRhodobacter capsulatus
NCBI taxonomy1061
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Conc0.1 mg/ml
Specimen Stateparticle
BufferpH: 8
Vitrification
Cryogen NameETHANE
InstrumentNONE
Imaging
MicroscopeJEOL 2010F
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Illumination ModeOTHER
Lens
MagnificationNominal: 60000
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderEucentric
ModelJEOL
Camera
Image Acquisition
#1
ScannerZEISS SCAI
Number of Digital Images6
Processing
Methodsingle particle reconstruction
3D reconstruction
Resolution By Author14 A
Resolution MethodFSC 0.5
Single Particle
Number of Class Averages526
Number of Projections17623
Applied SymmetryC3 (3 fold cyclic)
Atomic Model Fitting
Model #0
Refinement SpaceREAL
PDB Entry ID1G8P
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1678.xml (6.4 KB)
Map dataemd_1678.map.gz (1.9 MB)
Imagesemd_1678.jpg (29.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1678
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 26.5 KB