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- EMDB-46853: The Cryo-EM structure of recombinantly expressed apo hUGDH -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-46853
TitleThe Cryo-EM structure of recombinantly expressed apo hUGDH
Map dataFull map
Sample
  • Complex: Unliganded human UDP-Glucose Dehydrogenase
    • Protein or peptide: UDP-glucose 6-dehydrogenase
  • Ligand: water
KeywordsUnliganded human UDP-Glucose Dehydrogenase / OXIDOREDUCTASE
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: 2.06 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) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46853.png

Downloads & links

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Map

FileDownload / File: emd_46853.map.gz / Format: CCP4 / Size: 91.1 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.)
0.73 Å/pix.
x 288 pix.
= 210.24 Å		0.73 Å/pix.
x 288 pix.
= 210.24 Å		0.73 Å/pix.
x 288 pix.
= 210.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00814
Minimum - Maximum-0.045636717 - 0.08084641
Average (Standard dev.)0.00012588545 (±0.002303062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 210.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map1

Fileemd_46853_half_map_1.map
AnnotationHalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map2

Fileemd_46853_half_map_2.map
AnnotationHalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Unliganded human UDP-Glucose Dehydrogenase

EntireName: Unliganded human UDP-Glucose Dehydrogenase
Components
  • Complex: Unliganded human UDP-Glucose Dehydrogenase
    • Protein or peptide: UDP-glucose 6-dehydrogenase
  • Ligand: water

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Supramolecule #1: Unliganded human UDP-Glucose Dehydrogenase

SupramoleculeName: Unliganded human UDP-Glucose Dehydrogenase / 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: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 470 / 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

Concentration2.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
100.0 mMSodium ChlorideNaCl
1.0 mMDithiothreitol (DTT)
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 / Details: Glow discharged using Pelco Easiglow
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
DetailsApo human UGDH in 20 mM Hepes pH 7.5, 100 mM NaCl and 1 mM DTT with Fos-choline-8, fluorinated solution at a final concentration of 0.7 mM was added immediately before plunging to induce more particle orientations.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 35333 / Average electron dose: 46.44 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 / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
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: 1786206
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 91822
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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