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- EMDB-46854: The Cryo-EM structure of recombinantly expressed hUGDH in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-46854
TitleThe Cryo-EM structure of recombinantly expressed hUGDH in complex with UDP-4-keto-xylose
Map dataFull map
Sample
  • Complex: Human UDP-Glucose Dehydrogenase in complex with UDP-4-keto-xylose
    • Protein or peptide: UDP-glucose 6-dehydrogenase
  • Ligand: (2R,3R,4R)-3,4-dihydroxy-5-oxooxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)
  • Ligand: water
KeywordsHuman UDP-Glucose Dehydrogenase / UDP-4-keto-xylose / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


Formation of the active cofactor, UDP-glucuronate / : / UDP-glucose 6-dehydrogenase activity / UDP-glucose 6-dehydrogenase / UDP-glucuronate biosynthetic process / glycosaminoglycan biosynthetic process / heparan sulfate proteoglycan biosynthetic process / gastrulation with mouth forming second / protein hexamerization / neuron development ...Formation of the active cofactor, UDP-glucuronate / : / UDP-glucose 6-dehydrogenase activity / UDP-glucose 6-dehydrogenase / UDP-glucuronate biosynthetic process / glycosaminoglycan biosynthetic process / heparan sulfate proteoglycan biosynthetic process / gastrulation with mouth forming second / protein hexamerization / neuron development / NAD binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
UDP-glucose 6-dehydrogenase, eukaryotic type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain ...UDP-glucose 6-dehydrogenase, eukaryotic type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsKadirvelraj R / Walsh Jr RM / Wood ZW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM114298 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 3, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46854.png

Downloads & links

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Map

FileDownload / File: emd_46854.map.gz / Format: CCP4 / Size: 51.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 238 pix.
= 196.35 Å		0.83 Å/pix.
x 238 pix.
= 196.35 Å		0.83 Å/pix.
x 238 pix.
= 196.35 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.301
Minimum - Maximum-1.6357268 - 3.0180287
Average (Standard dev.)0.004535493 (±0.08306041)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions238238238
Spacing238238238
CellA=B=C: 196.34999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map2

Fileemd_46854_half_map_1.map
AnnotationHalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map1

Fileemd_46854_half_map_2.map
AnnotationHalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human UDP-Glucose Dehydrogenase in complex with UDP-4-keto-xylose

EntireName: Human UDP-Glucose Dehydrogenase in complex with UDP-4-keto-xylose
Components
  • Complex: Human UDP-Glucose Dehydrogenase in complex with UDP-4-keto-xylose
    • Protein or peptide: UDP-glucose 6-dehydrogenase
  • Ligand: (2R,3R,4R)-3,4-dihydroxy-5-oxooxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)
  • Ligand: water

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Supramolecule #1: Human UDP-Glucose Dehydrogenase in complex with UDP-4-keto-xylose

SupramoleculeName: Human UDP-Glucose Dehydrogenase in complex with UDP-4-keto-xylose
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.024 KDa

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Macromolecule #1: UDP-glucose 6-dehydrogenase

MacromoleculeName: UDP-glucose 6-dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: UDP-glucose 6-dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.093938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFEIKKICCI GAGYVGGPTC SVIAHMCPEI RVTVVDVNES RINAWNSPTL PIYEPGLKEV VESCRGKNLF FSTNIDDAIK EADLVFISV NTPTKTYGMG KGRAADLKYI EACARRIVQN SNGYKIVTEK STVPVRAAES IRRIFDANTK PNLNLQVLSN P EFLAEGTA ...String:
MFEIKKICCI GAGYVGGPTC SVIAHMCPEI RVTVVDVNES RINAWNSPTL PIYEPGLKEV VESCRGKNLF FSTNIDDAIK EADLVFISV NTPTKTYGMG KGRAADLKYI EACARRIVQN SNGYKIVTEK STVPVRAAES IRRIFDANTK PNLNLQVLSN P EFLAEGTA IKDLKNPDRV LIGGDETPEG QRAVQALCAV YEHWVPREKI LTTNTWSSEL SKLAANAFLA QRISSINSIS AL CEATGAD VEEVATAIGM DQRIGNKFLK ASVGFGGSCF QKDVLNLVYL CEALNLPEVA RYWQQVIDMN DYQRRRFASR IID SLFNTV TDKKIAILGF AFKKDTGDTR ESSSIYISKY LMDEGAHLHI YDPKVPREQI VVDLSHPGVS EDDQVSRLVT ISKD PYEAC DGAHAVVICT EWDMFKELDY ERIHKKMLKP AFIFDGRRVL DGLHNELQTI GFQIETIGKK VSSKRIPYAP SGEIP KFSL QDPPNKKPKV

UniProtKB: UDP-glucose 6-dehydrogenase

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Macromolecule #2: (2R,3R,4R)-3,4-dihydroxy-5-oxooxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dio...

MacromoleculeName: (2R,3R,4R)-3,4-dihydroxy-5-oxooxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1BCU
Molecular weightTheoretical: 534.26 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 193 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
100.0 mMSodium ChlorideNaCl
1.0 mMDTT
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
Details20 mM Hepes pH 7.5, 100 mM NaCl and 1 mM DTT.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 13500 / Average electron dose: 54.42 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4118676
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 3059917
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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