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- EMDB-3206: Revisited cryo-EM structure of Inducible lysine decarboxylase com... -

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Basic information

Entry
Database: EMDB / ID: EMD-3206
TitleRevisited cryo-EM structure of Inducible lysine decarboxylase complexed with LARA domain of RavA ATPase
Map dataReconstruction of E.coli Inducible lysine decarboxylase complexed with LARA domain of RavA ATPase
Sample
  • Sample: Complex between a decamer of inducible lysine decarboxylase LdcI and ten LARA domains of the AAA+ ATPase RavA
  • Protein or peptide: Inducible lysine decarboxylase
  • Protein or peptide: LARA domain of the AAA+ ATPase RavA
Keywordsacid-stress / lysine decarboxylase / ATPase / RavA / LARA / cage
Function / homology
Function and homology information


lysine decarboxylase / lysine catabolic process / lysine decarboxylase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / guanosine tetraphosphate binding / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / ATPase RavA / ATPase, RavA, C-terminal / ATPase RavA / ATPase RavA-like, AAA lid domain / MoxR domain / ATPase RavA, LARA domain / ATPase RavA, LARA domain superfamily / ATPase, RavA, C-terminal / AAA lid domain ...: / ATPase RavA / ATPase, RavA, C-terminal / ATPase RavA / ATPase RavA-like, AAA lid domain / MoxR domain / ATPase RavA, LARA domain / ATPase RavA, LARA domain superfamily / ATPase, RavA, C-terminal / AAA lid domain / MoxR domain in the MoxR-vWA-beta-propeller ternary systems / ATPase, RavA, LARA 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Inducible lysine decarboxylase / ATPase RavA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsKandiah E / Carriel D / Perard J / Malet H / Bacia M / Liu K / Chan SWS / Houry WA / 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 21, 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: 0.028
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fl2
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3206.tif

Downloads & links

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Map

FileDownload / File: emd_3206.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of E.coli Inducible lysine decarboxylase complexed with LARA domain of RavA ATPase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.46 Å/pix.
x 200 pix.
= 292.932 Å		1.46 Å/pix.
x 200 pix.
= 292.932 Å		1.46 Å/pix.
x 200 pix.
= 292.932 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.46466 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.04547018 - 0.06582431
Average (Standard dev.)0.0001311 (±0.00639349)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 292.932 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.464661.464661.46466
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z292.932292.932292.932
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.0450.0660.000

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Supplemental data

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Sample components

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Entire : Complex between a decamer of inducible lysine decarboxylase LdcI ...

EntireName: Complex between a decamer of inducible lysine decarboxylase LdcI and ten LARA domains of the AAA+ ATPase RavA
Components
  • Sample: Complex between a decamer of inducible lysine decarboxylase LdcI and ten LARA domains of the AAA+ ATPase RavA
  • Protein or peptide: Inducible lysine decarboxylase
  • Protein or peptide: LARA domain of the AAA+ ATPase RavA

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Supramolecule #1000: Complex between a decamer of inducible lysine decarboxylase LdcI ...

SupramoleculeName: Complex between a decamer of inducible lysine decarboxylase LdcI and ten LARA domains of the AAA+ ATPase RavA
type: sample / ID: 1000
Oligomeric state: One homodecamer of LdcI bound to ten monomers of LARA domains of the AAA+ ATPase RavA
Number unique components: 2
Molecular weightExperimental: 936 KDa / Theoretical: 936 KDa

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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 / Location in cell: cytoplasm
Molecular weightExperimental: 81.2 KDa / Theoretical: 81.2 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: MG1655 / Recombinant plasmid: pET22b
SequenceUniProtKB: Inducible lysine decarboxylase / GO: lysine catabolic process / InterPro: Ornithine/lysine/arginine decarboxylase

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Macromolecule #2: LARA domain of the AAA+ ATPase RavA

MacromoleculeName: LARA domain of the AAA+ ATPase RavA / type: protein_or_peptide / ID: 2 / Name.synonym: LARA domain of RavA / Number of copies: 10 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12 / Location in cell: cytoplasm
Molecular weightExperimental: 12.405 KDa / Theoretical: 12.405 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Gold pLysS / Recombinant plasmid: p11
SequenceUniProtKB: ATPase RavA / GO: ATP hydrolysis activity / InterPro: ATPase RavA

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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

Concentration0.6 mg/mL
BufferpH: 6.5
Details: 50mM MES pH 6.5, 100mM NaCl, 0.2mM PLP, 1mM DTT, 0.01% glutaraldehyde
GridDetails: Quantifoil 400 mesh 2/1 Glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 91 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 90 K / Max: 92 K / Average: 91 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Legacy - Electron beam tilt params: 0
DetailsAutomatic data acquisition with FEI EPU software
DateSep 14, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 911 / Average electron dose: 20 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51660 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 51660
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

CTF correctionDetails: individual particle with full CTF correction after first peak
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: OTHER / Software - Name: CTFFIND3, EMAN, boxer, IMAGIC, FPM, RELION / Number images used: 23540
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3n75


Chain - Chain ID: A
SoftwareName: Chimera, IMODFIT
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation
Output model

PDB-5fl2:
Revisited cryo-EM structure of Inducible lysine decarboxylase complexed with LARA domain of RavA ATPase

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Atomic model buiding 2

Initial modelPDB ID:

3nbx


Chain - Chain ID: X
SoftwareName: SITUS
DetailsThe residues 332-437 corresponding to the RavA LARA domain were fitted
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation
Output model

PDB-5fl2:
Revisited cryo-EM structure of Inducible lysine decarboxylase complexed with LARA domain of RavA ATPase

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