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- EMDB-3204: Structures of E.coli lysine decarboxylases -

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Basic information

Entry
Database: EMDB / ID: EMD-3204
TitleStructures of E.coli lysine decarboxylases
Map dataReconstruction of active induced Lysine decarboxylase from E.coli
Sample
  • Sample: E.coli Induced Lysine Decarboxylase at active pH
  • Protein or peptide: Inducible Lysine decarboxylase
Keywordsacid-stress / lysine decarboxylase / RavA / cage
Function / homology
Function and homology information


lysine decarboxylase / lysine catabolic process / lysine decarboxylase activity / guanosine tetraphosphate binding / identical protein binding / cytoplasm
Similarity search - Function
Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain ...Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Inducible lysine decarboxylase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsKandiah E / Carriel D / Perard J / Malet H / Bacia M / Liu K / Chan WSS / Houry AW / Ollagnier de Choudens S / Elsen S / Gutsche I
CitationJournal: Elife / Year: 2014
Title: Assembly principles of a unique cage formed by hexameric and decameric E. coli proteins.
Authors: Hélène Malet / Kaiyin Liu / Majida El Bakkouri / Sze Wah Samuel Chan / Gregory Effantin / Maria Bacia / Walid A Houry / Irina Gutsche /
Abstract: A 3.3 MDa macromolecular cage between two Escherichia coli proteins with seemingly incompatible symmetries-the hexameric AAA+ ATPase RavA and the decameric inducible lysine decarboxylase LdcI-is ...A 3.3 MDa macromolecular cage between two Escherichia coli proteins with seemingly incompatible symmetries-the hexameric AAA+ ATPase RavA and the decameric inducible lysine decarboxylase LdcI-is reconstructed by cryo-electron microscopy to 11 Å resolution. Combined with a 7.5 Å resolution reconstruction of the minimal complex between LdcI and the LdcI-binding domain of RavA, and the previously solved crystal structures of the individual components, this work enables to build a reliable pseudoatomic model of this unusual architecture and to identify conformational rearrangements and specific elements essential for complex formation. The design of the cage created via lateral interactions between five RavA rings is unique for the diverse AAA+ ATPase superfamily.
History
DepositionOct 20, 2015-
Header (metadata) releaseNov 4, 2015-
Map releaseSep 21, 2016-
UpdateSep 21, 2016-
Current statusSep 21, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0162
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0162
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fkx
  • Surface level: 0.0162
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3402.png

Downloads & links

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Map

FileDownload / File: emd_3204.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of active induced Lysine decarboxylase from E.coli
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 256 pix.
= 303.616 Å		1.19 Å/pix.
x 256 pix.
= 303.616 Å		1.19 Å/pix.
x 256 pix.
= 303.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.186 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0162 / Movie #1: 0.0162
Minimum - Maximum-0.03683831 - 0.04733011
Average (Standard dev.)0.00005259 (±0.00360797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 303.616 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1861.1861.186
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z303.616303.616303.616
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.0370.0470.000

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Supplemental data

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Sample components

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Entire : E.coli Induced Lysine Decarboxylase at active pH

EntireName: E.coli Induced Lysine Decarboxylase at active pH
Components
  • Sample: E.coli Induced Lysine Decarboxylase at active pH
  • Protein or peptide: Inducible Lysine decarboxylase

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Supramolecule #1000: E.coli Induced Lysine Decarboxylase at active pH

SupramoleculeName: E.coli Induced Lysine Decarboxylase at active pH / type: sample / ID: 1000 / Oligomeric state: Homodecamer / Number unique components: 1
Molecular weightExperimental: 81.2 KDa / Theoretical: 81.2 KDa / Method: Size exclusion

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Macromolecule #1: Inducible Lysine decarboxylase

MacromoleculeName: Inducible Lysine decarboxylase / type: protein_or_peptide / ID: 1 / Name.synonym: LdcI / Number of copies: 10 / Oligomeric state: Homodecamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12 / synonym: E.coli
Molecular weightExperimental: 81.2 KDa / Theoretical: 81.2 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: MG1655
SequenceUniProtKB: Inducible lysine decarboxylase / GO: lysine catabolic process / InterPro: Ornithine/lysine/arginine decarboxylase

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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

Concentration2 mg/mL
BufferpH: 6.2
Details: 25 mM MES, 100 mM NaCl, 0.2 mM PLP, 1 mM DTT, pH 6.2
GridDetails: glow-discharged quantifoil grids 300 mesh 2/1
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 91 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 2.5 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 90 K / Max: 92 K / Average: 91 K
Alignment procedureLegacy - Electron beam tilt params: 0
DateJun 2, 2014
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 134 / Average electron dose: 25 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 59000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.9 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: GATAN HELIUM
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsReconstruction was done using RELION v1.3 with full CTF correction after first peak.
CTF correctionDetails: each particle; full CTF correction after first peak
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 44207

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