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- EMDB-29870: Human IMPDH2 mutant - L245P, treated with GTP, ATP, IMP, and NAD+... -

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Basic information

Entry
Database: EMDB / ID: EMD-29870
TitleHuman IMPDH2 mutant - L245P, treated with GTP, ATP, IMP, and NAD+; bent filament segment reconstruction
Map dataMap from PHENIX density modification. Used to build model.
Sample
  • Complex: Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P mutant, bound to GTP, ATP, IMP, and NAD+
    • Protein or peptide: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2
KeywordsFilament / Dehydrogenase / CBS domain / Bateman domain / purine biosynthesis / OXIDOREDUCTASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsO'Neill AG / Kollman JM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118396 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008268 United States
CitationJournal: J Comput Chem / Year: 2004
Title: UCSF Chimera--a visualization system for exploratory research and analysis.
Authors: Eric F Pettersen / Thomas D Goddard / Conrad C Huang / Gregory S Couch / Daniel M Greenblatt / Elaine C Meng / Thomas E Ferrin /
Abstract: The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and ...The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.
History
DepositionFeb 21, 2023-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29870.png

Downloads & links

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Map

FileDownload / File: emd_29870.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap from PHENIX density modification. Used to build model.
Voxel sizeX=Y=Z: 0.843 Å
Density
Contour LevelBy AUTHOR: 0.48
Minimum - Maximum-7.8762755 - 15.922696999999999
Average (Standard dev.)0.000000000000687 (±0.2743121)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 337.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29870_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map from Relion Postprocessing.

Fileemd_29870_additional_1.map
AnnotationMap from Relion Postprocessing.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29870_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29870_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P muta...

EntireName: Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P mutant, bound to GTP, ATP, IMP, and NAD+
Components
  • Complex: Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P mutant, bound to GTP, ATP, IMP, and NAD+
    • Protein or peptide: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2

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Supramolecule #1: Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P muta...

SupramoleculeName: Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P mutant, bound to GTP, ATP, IMP, and NAD+
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: 5 uM enzyme was mixed with 20 mM GTP, 1 mM ATP, 1 mM MgCl2, 3 mM IMP, and 5 mM NAD+.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2

MacromoleculeName: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: IMP dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SEFELMADYL ISGGTSYVPD DGLTAQQLFN CGDGLTYNDF LILPGYIDFT ADQVDLTSAL TKKITLKTPL VSSPMDTVTE AGMAIAMAL TGGIGFIHHN CTPEFQANEV RKVKKYEQGF ITDPVVLSPK DRVRDVFEAK ARHGFCGIPI TDTGRMGSRL V GIISSRDI ...String:
SEFELMADYL ISGGTSYVPD DGLTAQQLFN CGDGLTYNDF LILPGYIDFT ADQVDLTSAL TKKITLKTPL VSSPMDTVTE AGMAIAMAL TGGIGFIHHN CTPEFQANEV RKVKKYEQGF ITDPVVLSPK DRVRDVFEAK ARHGFCGIPI TDTGRMGSRL V GIISSRDI DFLKEEEHDC FLEEIMTKRE DLVVAPAGIT LKEANEILQR SKKGKLPIVN EDDELVAIIA RTDLKKNRDY PL ASKDAKK QLPCGAAIGT HEDDKYRLDL LAQAGVDVVV LDSSQGNSIF QINMIKYIKD KYPNLQVIGG NVVTAAQAKN LID AGVDAL RVGMGSGSIC ITQEVLACGR PQATAVYKVS EYARRFGVPV IADGGIQNVG HIAKALALGA STVMMGSLLA ATTE APGEY FFSDGIRLKK YRGMGSLDAM DKHLSSQNRY FSEADKIKVA QGVSGAVQDK GSIHKFVPYL IAGIQHSCQD IGAKS LTQV RAMMYSGELK FEKRTSSAQV EGGVHSLHSY EKRLF

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 2967 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.28 µm / Nominal defocus min: 1.74 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1421990
Startup modelType of model: EMDB MAP
EMDB ID:

20701


Details: Map was low-pass filtered
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: OTHER / Software: (Name: RELION (ver. 3.1), PHENIX (ver. 1.18.2))
Details: FSCref 0.5 cut-off from PHENIX density modification
Number images used: 91716
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

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