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- EMDB-1319: Octomeric pyruvate-ferredoxin oxidoreductase from Desulfovibrio v... -

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Basic information

Entry
Database: EMDB / ID: EMD-1319
TitleOctomeric pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris.
Map datapyrovat-ferredoxin oxidoreductase from Desulfovibrio vulgaris Hildenborough
Sample
  • Sample: pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris HildenboroughPyruvate synthase
  • Protein or peptide: pyruvate-ferredoxin oxidoreductasePyruvate synthase
Biological speciesDesulfovibrio vulgaris str. Hildenborough (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 Å
AuthorsGarczarek F / Dong M / Typke D / Witkowska E / Hazen TC / Nogales E / Glaeser R
CitationJournal: J Struct Biol / Year: 2007
Title: Octomeric pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris.
Authors: Florian Garczarek / Ming Dong / Dieter Typke / H Ewa Witkowska / Terry C Hazen / Eva Nogales / Mark D Biggin / Robert M Glaeser /
Abstract: Pyruvate-ferredoxin oxidoreductatse (PFOR) carries out the central step in oxidative decarboxylation of pyruvate to acetyl-CoA. We have purified this enzyme from Desulfovibrio vulgaris Hildenborough ...Pyruvate-ferredoxin oxidoreductatse (PFOR) carries out the central step in oxidative decarboxylation of pyruvate to acetyl-CoA. We have purified this enzyme from Desulfovibrio vulgaris Hildenborough (DvH) as part of a systematic characterization of as many multiprotein complexes as possible for this organism, and the three-dimensional structure of this enzyme has been determined by a combination of electron microscopy (EM), single particle image analysis, homology modeling and computational molecular docking. Our results show that the 1MDa DvH PFOR complex is a homo-octomer, or more precisely, a tetramer of the dimeric form of the related enzyme found in Desulfovibrio africanus (Da), with which it shares a sequence identity of 69%. Our homology model of the DvH PFOR dimer is based on the Da PFOR X-ray structure. Docking of this model into our 17A resolution EM-reconstruction of negatively stained DvH PFOR octomers strongly suggests that the difference in oligomerization state for the two species is due to the insertion of a single valine residue (Val383) within a surface loop of the DvH enzyme. This study demonstrates that the strategy of intermediate resolution EM reconstruction coupled to homology modeling and docking can be powerful enough to infer the functionality of single amino acid residues.
History
DepositionDec 27, 2006-
Header (metadata) releaseFeb 5, 2007-
Map releaseJun 21, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.772935571
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.772935571
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1319.gif

Downloads & links

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Map

FileDownload / File: emd_1319.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpyrovat-ferredoxin oxidoreductase from Desulfovibrio vulgaris Hildenborough
Voxel sizeX=Y=Z: 2.56 Å
Density
Contour Level1: 1.0 / Movie #1: 1.7729356
Minimum - Maximum-7.60225 - 10.776400000000001
Average (Standard dev.)0.00000000515461 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 409.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.562.562.56
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z409.600409.600409.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-150-149
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-7.60210.7760.000

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Supplemental data

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Sample components

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Entire : pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris Hi...

EntireName: pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris HildenboroughPyruvate synthase
Components
  • Sample: pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris HildenboroughPyruvate synthase
  • Protein or peptide: pyruvate-ferredoxin oxidoreductasePyruvate synthase

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Supramolecule #1000: pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris Hi...

SupramoleculeName: pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris Hildenborough
type: sample / ID: 1000 / Oligomeric state: homooctomer / Number unique components: 1
Molecular weightTheoretical: 1.056 MDa

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Macromolecule #1: pyruvate-ferredoxin oxidoreductase

MacromoleculeName: pyruvate-ferredoxin oxidoreductase / type: protein_or_peptide / ID: 1 / Name.synonym: PFOR / Number of copies: 8 / Oligomeric state: homooctomer / Recombinant expression: Yes
Source (natural)Organism: Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain: ATCC 29579
Molecular weightExperimental: 132 MDa / Theoretical: 132 MDa
Recombinant expressionOrganism: Desulfovibrio vulgaris str. Hildenborough (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

Concentration0.05 mg/mL
BufferpH: 7.6 / Details: 10mM HEPES, 2mM DTT, 0.01% NP40
StainingType: NEGATIVE / Details: 5% ammonium molybdate, 1% trehalose, pH7
GridDetails: 400 mesh copper grid coated with carbon layer
VitrificationCryogen name: NONE

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 49700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 6.2 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 50000
Sample stageSpecimen holder: side entry / Specimen holder model: OTHER
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 12.7 µm / Number real images: 19

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Image processing

CTF correctionDetails: defocus groups
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, SPIDER / Number images used: 12402

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