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- EMDB-3163: Single-particle reconstruction of negatively stained SufBCD -

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Basic information

Entry
Database: EMDB / ID: EMD-3163
TitleSingle-particle reconstruction of negatively stained SufBCD
Map dataReconstruction of SufBCD. The particle images were low-pass filtered before refinement. The FSC that was calculated using eotest shows higher values than 0.5 every frequencies.
Sample
  • Sample: SufBCD
  • Protein or peptide: SufBCD
KeywordsIron-sulfur cluster / ABC-ATPase / Suf machinery / ABC-transporter
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 30.0 Å
AuthorsHirabayashi K / Yuda E / Tanaka N / Katayama S / Iwasaki K / Matsumoto T / Kurisu G / Outten FW / Fukuyama K / Takahashi Y / Wada K
CitationJournal: J Biol Chem / Year: 2015
Title: Functional Dynamics Revealed by the Structure of the SufBCD Complex, a Novel ATP-binding Cassette (ABC) Protein That Serves as a Scaffold for Iron-Sulfur Cluster Biogenesis.
Authors: Kei Hirabayashi / Eiki Yuda / Naoyuki Tanaka / Sumie Katayama / Kenji Iwasaki / Takashi Matsumoto / Genji Kurisu / F Wayne Outten / Keiichi Fukuyama / Yasuhiro Takahashi / Kei Wada /
Abstract: ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC ...ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC transporters and structural maintenance of chromosome proteins, but also in iron-sulfur (Fe-S) cluster biogenesis. A novel type of ABC protein, the SufBCD complex, functions in the biosynthesis of nascent Fe-S clusters in almost all Eubacteria and Archaea, as well as eukaryotic chloroplasts. In this study, we determined the first crystal structure of the Escherichia coli SufBCD complex, which exhibits the common architecture of ABC proteins: two ABC ATPase components (SufC) with function-specific components (SufB-SufD protomers). Biochemical and physiological analyses based on this structure provided critical insights into Fe-S cluster assembly and revealed a dynamic conformational change driven by ABC ATPase activity. We propose a molecular mechanism for the biogenesis of the Fe-S cluster in the SufBCD complex.
History
DepositionSep 24, 2015-
Header (metadata) releaseOct 14, 2015-
Map releaseOct 28, 2015-
UpdateJan 13, 2016-
Current statusJan 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3163.png

Downloads & links

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Map

FileDownload / File: emd_3163.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of SufBCD. The particle images were low-pass filtered before refinement. The FSC that was calculated using eotest shows higher values than 0.5 every frequencies.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 100 pix.
= 220. Å		2.2 Å/pix.
x 100 pix.
= 220. Å		2.2 Å/pix.
x 100 pix.
= 220. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 5.31 / Movie #1: 2.5
Minimum - Maximum-2.65798402 - 9.84889793
Average (Standard dev.)0.0 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z220.000220.000220.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-2.6589.8490.000

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Supplemental data

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Sample components

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Entire : SufBCD

EntireName: SufBCD
Components
  • Sample: SufBCD
  • Protein or peptide: SufBCD

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Supramolecule #1000: SufBCD

SupramoleculeName: SufBCD / type: sample / ID: 1000 / Details: The sample was monodisperse.
Oligomeric state: One of a couple of the SufC subunits binds to the SufB protomer of the heterodimeric complex of SufB and SufD. The other SufC subunit binds to the SufD protomer.
Number unique components: 3
Molecular weightExperimental: 160 KDa / Theoretical: 156.7 KDa
Method: Size-exclusion chromatography and Dynamic light scattering

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Macromolecule #1: SufBCD

MacromoleculeName: SufBCD / type: protein_or_peptide / ID: 1
Details: Carbon coated grid. Negatively staining with uranyl acetate.
Oligomeric state: Heterotetramer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Location in cell: Cytosol
Molecular weightExperimental: 160 KDa / Theoretical: 156.7 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

StainingType: NEGATIVE / Details: 2% Uranyl acetate
GridDetails: Carbon coated grid.
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeHITACHI H-9500SD
TemperatureAverage: 293 K
DateJan 21, 2009
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k) / Digitization - Sampling interval: 24 µm
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 109091 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.8 mm / Nominal magnification: 80000
Sample stageSpecimen holder: Room temperature / Specimen holder model: OTHER

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Image processing

CTF correctionDetails: No correction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: EMAN1
Details: Particles images were lowpass-filtered at 30A before refinement. Therefore, FSC shows higher values than 0.5 in every frequency ranges.So, we think that, in our case, FSC is not appropriate ...Details: Particles images were lowpass-filtered at 30A before refinement. Therefore, FSC shows higher values than 0.5 in every frequency ranges.So, we think that, in our case, FSC is not appropriate to use resolution determination. We used eotest of EMAN. We do not know if this corresponds to FCS type "even/odd maps were refined agains the same model (semi-independedt) or not.
Number images used: 7146

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