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- EMDB-55549: GDH in complex with compound G2, processed with cryoPARES -

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Basic information

Entry
Database: EMDB / ID: EMD-55549
TitleGDH in complex with compound G2, processed with cryoPARES
Map dataRelion post-processed map of half-maps generated by cryoPARES
Sample
  • Complex: L-Glutamic Dehydrogenase 1 (GDH1)
    • Protein or peptide: Glutamate dehydrogenase 1, mitochondrial
  • Ligand: 2-azanyl-1,3-benzothiazole-6-sulfonamide
KeywordsGDH / Fragment / ligand / cryoPARES / OXIDOREDUCTASE
Function / homology
Function and homology information


L-glutamate dehydrogenase [NAD(P)+] activity / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / L-glutamate dehydrogenase (NADP+) activity / L-glutamate dehydrogenase (NAD+) activity / L-glutamine metabolic process / L-glutamate catabolic process / mitochondrial inner membrane / endoplasmic reticulum / mitochondrion / identical protein binding
Similarity search - Function
NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glutamate dehydrogenase 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSaur M / Sanchez-Garcia R
Funding support1 items
OrganizationGrant numberCountry
Other privateSIPD
CitationJournal: BioRXiv
Title: Supervised Deep Learning for Efficient Cryo-EM Image Alignment in Drug Discovery with cryoPARES
Authors: Sanchez-Garcia R / Berndt A / Apelbaum A / Reeks J / Williams PA / Poelking C / Deane CM / Saur M
History
DepositionNov 3, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55549.png

Downloads & links

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Map

FileDownload / File: emd_55549.map.gz / Format: CCP4 / Size: 172.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRelion post-processed map of half-maps generated by cryoPARES
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 356 pix.
= 355.69 Å		1 Å/pix.
x 356 pix.
= 355.69 Å		1 Å/pix.
x 356 pix.
= 355.69 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99913 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.062233146 - 0.13888055
Average (Standard dev.)0.00015613055 (±0.002898711)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions356356356
Spacing356356356
CellA=B=C: 355.69028 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55549_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 generated by cryoPARES.

Fileemd_55549_half_map_1.map
AnnotationHalf-map 1 generated by cryoPARES.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 generated by cryoPARES.

Fileemd_55549_half_map_2.map
AnnotationHalf-map 2 generated by cryoPARES.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : L-Glutamic Dehydrogenase 1 (GDH1)

EntireName: L-Glutamic Dehydrogenase 1 (GDH1)
Components
  • Complex: L-Glutamic Dehydrogenase 1 (GDH1)
    • Protein or peptide: Glutamate dehydrogenase 1, mitochondrial
  • Ligand: 2-azanyl-1,3-benzothiazole-6-sulfonamide

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Supramolecule #1: L-Glutamic Dehydrogenase 1 (GDH1)

SupramoleculeName: L-Glutamic Dehydrogenase 1 (GDH1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Hexameric complex of L-Glutamic Dehydrogenase from bovine liver type II; Purchased from Sigma-Aldrich, G2626-100mg as 50% solution in glycerol, dialysed and subjected to size exclusion chromatography
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: liver

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Macromolecule #1: Glutamate dehydrogenase 1, mitochondrial

MacromoleculeName: Glutamate dehydrogenase 1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: glutamate dehydrogenase [NAD(P)+]
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: liver
Molecular weightTheoretical: 54.880406 KDa
SequenceString: DPNFFKMVEG FFDRGASIVE DKLVEDLKTR ETEEQKRNRV RSILRIIKPC NHVLSLSFPI RRDDGSWEVI EGYRAQHSQH RTPCKGGIR YSTDVSVDEV KALASLMTYK CAVVDVPFGG AKAGVKINPK NYTDNELEKI TRRFTMELAK KGFIGPGVDV P APDMSTGE ...String:
DPNFFKMVEG FFDRGASIVE DKLVEDLKTR ETEEQKRNRV RSILRIIKPC NHVLSLSFPI RRDDGSWEVI EGYRAQHSQH RTPCKGGIR YSTDVSVDEV KALASLMTYK CAVVDVPFGG AKAGVKINPK NYTDNELEKI TRRFTMELAK KGFIGPGVDV P APDMSTGE REMSWIADTY ASTIGHYDIN AHACVTGKPI SQGGIHGRIS ATGRGVFHGI ENFINEASYM SILGMTPGFG DK TFVVQGF GNVGLHSMRY LHRFGAKCIT VGESDGSIWN PDGIDPKELE DFKLQHGTIL GFPKAKIYEG SILEVDCDIL IPA ASEKQL TKSNAPRVKA KIIAEGANGP TTPEADKIFL ERNIMVIPDL YLNAGGVTVS YFEWLKNLNH VSYGRLTFKY ERDS NYHLL MSVQESLERK FGKHGGTIPI VPTAEFQDRI SGASEKDIVH SGLAYTMERS ARQIMRTAMK YNLGLDLRTA AYVNA IEKV FRVYNEAGV

UniProtKB: Glutamate dehydrogenase 1, mitochondrial

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Macromolecule #2: 2-azanyl-1,3-benzothiazole-6-sulfonamide

MacromoleculeName: 2-azanyl-1,3-benzothiazole-6-sulfonamide / type: ligand / ID: 2 / Number of copies: 18 / Formula: A1JTL
Molecular weightTheoretical: 229.279 Da

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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

Concentration0.35 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
200.0 mMHEPESHEPES
150.0 mMNaClSodium Chloride
5.0 %DMSODMSO
0.001 %Tween-20Tween-20
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE OXIDE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 933 / Average exposure time: 59.98 sec. / Average electron dose: 62.51 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: 120000
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

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 120465
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: OTHER / Details: cryoPARES

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9t4x:
GDH in complex with compound G2, processed with cryoPARES

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