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- EMDB-29848: Human IMPDH2 mutant - L245P, treated with ATP, IMP, and NAD+; ext... -

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Basic information

Entry
Database: EMDB / ID: EMD-29848
TitleHuman IMPDH2 mutant - L245P, treated with ATP, IMP, and NAD+; extended 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 ATP, IMP, and NAD+
    • Protein or peptide: Inosine-5'-monophosphate dehydrogenase 2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: INOSINIC ACID
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
KeywordsFilament / Dehydrogenase / CBS domain / Bateman domain / purine biosynthesis / OXIDOREDUCTASE
Function / homology
Function and homology information


'de novo' XMP biosynthetic process / lymphocyte proliferation / Purine ribonucleoside monophosphate biosynthesis / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / peroxisomal membrane / cellular response to interleukin-4 ...'de novo' XMP biosynthetic process / lymphocyte proliferation / Purine ribonucleoside monophosphate biosynthesis / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / peroxisomal membrane / cellular response to interleukin-4 / circadian rhythm / secretory granule lumen / ficolin-1-rich granule lumen / Potential therapeutics for SARS / nucleotide binding / Neutrophil degranulation / DNA binding / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
Inosine-5'-monophosphate dehydrogenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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 17, 2023-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29848.png

Downloads & links

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Map

FileDownload / File: emd_29848.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.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 400 pix.
= 337.2 Å		0.84 Å/pix.
x 400 pix.
= 337.2 Å		0.84 Å/pix.
x 400 pix.
= 337.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.843 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.43
Minimum - Maximum-6.9247212 - 13.181594
Average (Standard dev.)0.000000000000083 (±0.28035796)
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_29848_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_29848_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_29848_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_29848_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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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 ATP, IMP, and NAD+
Components
  • Complex: Filament of Inosine-5'-monophosphate dehydrogenase 2 - L245P mutant, bound to ATP, IMP, and NAD+
    • Protein or peptide: Inosine-5'-monophosphate dehydrogenase 2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: INOSINIC ACID
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

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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 ATP, IMP, and NAD+
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: 5 uM enzyme was mixed with 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 / Number of copies: 8 / Enantiomer: LEVO / EC number: IMP dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.464453 KDa
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

UniProtKB: Inosine-5'-monophosphate dehydrogenase 2

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 16 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: INOSINIC ACID

MacromoleculeName: INOSINIC ACID / type: ligand / ID: 3 / Number of copies: 8 / Formula: IMP
Molecular weightTheoretical: 348.206 Da
Chemical component information

ChemComp-I:
INOSINIC ACID

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Macromolecule #4: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 8 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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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: 2648 / 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: 0.27 µm / Nominal defocus min: 1.71 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: 1893802
Startup modelType of model: EMDB MAP
EMDB ID:

20688


Details: Map was low-pass filtered
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.6 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: 54304
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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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8g8f:
Human IMPDH2 mutant - L245P, treated with ATP, IMP, and NAD+; extended filament segment reconstruction

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