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- EMDB-8692: Human Inosine Monophosphate Dehydrogenase 2 (hIMPDH2), Y12A mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-8692
TitleHuman Inosine Monophosphate Dehydrogenase 2 (hIMPDH2), Y12A mutant
Map datahuman inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry
Sample
  • Complex: human inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsKollman JK / Johnson MC / Burrell AL
CitationJournal: Mol Biol Cell / Year: 2017
Title: Reconstituted IMPDH polymers accommodate both catalytically active and inactive conformations.
Authors: Sajitha A Anthony / Anika L Burrell / Matthew C Johnson / Krisna C Duong-Ly / Yin-Ming Kuo / Jacqueline C Simonet / Peter Michener / Andrew Andrews / Justin M Kollman / Jeffrey R Peterson /
Abstract: Several metabolic enzymes undergo reversible polymerization into macromolecular assemblies. The function of these assemblies is often unclear but in some cases they regulate enzyme activity and ...Several metabolic enzymes undergo reversible polymerization into macromolecular assemblies. The function of these assemblies is often unclear but in some cases they regulate enzyme activity and metabolic homeostasis. The guanine nucleotide biosynthetic enzyme inosine monophosphate dehydrogenase (IMPDH) forms octamers that polymerize into helical chains. In mammalian cells, IMPDH filaments can associate into micron-length assemblies. Polymerization and enzyme activity are regulated in part by binding of purine nucleotides to an allosteric regulatory domain. ATP promotes octamer polymerization, whereas GTP promotes a compact, inactive conformation whose ability to polymerize is unknown. Also unclear is whether polymerization directly alters IMPDH catalytic activity. To address this, we identified point mutants of human IMPDH2 that either prevent or promote polymerization. Unexpectedly, we found that polymerized and non-assembled forms of recombinant IMPDH have comparable catalytic activity, substrate affinity, and GTP sensitivity and validated this finding in cells. Electron microscopy revealed that substrates and allosteric nucleotides shift the equilibrium between active and inactive conformations in both the octamer and the filament. Unlike other metabolic filaments, which selectively stabilize active or inactive conformations, recombinant IMPDH filaments accommodate multiple states. These conformational states are finely tuned by substrate availability and purine balance, while polymerization may allow cooperative transitions between states.
History
DepositionApr 17, 2017-
Header (metadata) releaseMay 3, 2017-
Map releaseAug 23, 2017-
UpdateAug 23, 2017-
Current statusAug 23, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8692.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry
Voxel sizeX=Y=Z: 2.52 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.08565029 - 0.19400139
Average (Standard dev.)0.0010673945 (±0.014417902)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 252.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.522.522.52
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0860.1940.001

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Supplemental data

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Sample components

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Entire : human inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry

EntireName: human inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry
Components
  • Complex: human inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry

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Supramolecule #1: human inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry

SupramoleculeName: human inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3)

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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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Negative stain reconstruction
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6603
FSC plot (resolution estimation)

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