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- EMDB-10743: Low resolution structure of Glutaconyl-CoA Decarboxylase from Clo... -

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Basic information

Entry
Database: EMDB / ID: EMD-10743
TitleLow resolution structure of Glutaconyl-CoA Decarboxylase from Clostridium symbiosum
Map data
Sample
  • Complex: Na+-Translocating Glutaconyl-CoA Decarboxylase
Biological speciesClostridium symbiosum (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
AuthorsVitt S
Funding support1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)
CitationJournal: Front Microbiol / Year: 2020
Title: Molecular and Low-Resolution Structural Characterization of the Na-Translocating Glutaconyl-CoA Decarboxylase From .
Authors: Stella Vitt / Simone Prinz / Nils Hellwig / Nina Morgner / Ulrich Ermler / Wolfgang Buckel /
Abstract: Some anaerobic bacteria use biotin-dependent Na-translocating decarboxylases (Bdc) of β-keto acids or their thioester analogs as key enzymes in their energy metabolism. Glutaconyl-CoA decarboxylase ...Some anaerobic bacteria use biotin-dependent Na-translocating decarboxylases (Bdc) of β-keto acids or their thioester analogs as key enzymes in their energy metabolism. Glutaconyl-CoA decarboxylase (Gcd), a member of this protein family, drives the endergonic translocation of Na across the membrane with the exergonic decarboxylation of glutaconyl-CoA (Δ ' ≈-30 kJ/mol) to crotonyl-CoA. Here, we report on the molecular characterization of Gcd from based on native PAGE, size exclusion chromatography (SEC) and laser-induced liquid bead ion desorption mass spectrometry (LILBID-MS). The obtained molecular mass of ca. 400 kDa fits to the DNA sequence-derived mass of 379 kDa with a subunit composition of 4 GcdA (65 kDa), 2 GcdB (35 kDa), GcdC1 (15 kDa), GcdC2 (14 kDa), and 2 GcdD (10 kDa). Low-resolution structural information was achieved from preliminary electron microscopic (EM) measurements, which resulted in a 3D reconstruction model based on negative-stained particles. The Gcd structure is built up of a membrane-spanning base primarily composed of the GcdB dimer and a solvent-exposed head with the GcdA tetramer as major component. Both globular parts are bridged by a linker presumably built up of segments of GcdC1, GcdC2 and the 2 GcdDs. The structure of the highly mobile Gcd complex represents a template for the global architecture of the Bdc family.
History
DepositionMar 11, 2020-
Header (metadata) releaseMay 6, 2020-
Map releaseMay 6, 2020-
UpdateMay 6, 2020-
Current statusMay 6, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0873
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0873
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10743.png

Downloads & links

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Map

FileDownload / File: emd_10743.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.68 Å/pix.
x 224 pix.
= 600.32 Å		2.68 Å/pix.
x 224 pix.
= 600.32 Å		2.68 Å/pix.
x 224 pix.
= 600.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0873 / Movie #1: 0.0873
Minimum - Maximum-0.0020134882 - 0.361036
Average (Standard dev.)0.0019810088 (±0.019746276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 600.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.682.682.68
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z600.320600.320600.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0020.3610.002

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Supplemental data

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Sample components

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Entire : Na+-Translocating Glutaconyl-CoA Decarboxylase

EntireName: Na+-Translocating Glutaconyl-CoA Decarboxylase
Components
  • Complex: Na+-Translocating Glutaconyl-CoA Decarboxylase

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Supramolecule #1: Na+-Translocating Glutaconyl-CoA Decarboxylase

SupramoleculeName: Na+-Translocating Glutaconyl-CoA Decarboxylase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Clostridium symbiosum (bacteria)

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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

BufferpH: 7
StainingType: NEGATIVE / Material: uranyl formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: OTHER / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36009
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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