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- PDB-9t4w: GDH in complex with compound G1, processed with cryoPARES -

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Basic information

Entry
Database: PDB / ID: 9t4w
TitleGDH in complex with compound G1, processed with cryoPARES
ComponentsGlutamate dehydrogenase 1, mitochondrial
KeywordsOXIDOREDUCTASE / GDH / Fragment / ligand / cryoPARES
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSaur, M. / Sanchez-Garcia, R.
Funding support1items
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, P.A. / Poelking, C. / Deane, C.M. / Saur, M.
History
DepositionNov 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate dehydrogenase 1, mitochondrial
B: Glutamate dehydrogenase 1, mitochondrial
C: Glutamate dehydrogenase 1, mitochondrial
D: Glutamate dehydrogenase 1, mitochondrial
E: Glutamate dehydrogenase 1, mitochondrial
F: Glutamate dehydrogenase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,77824
Polymers329,2826
Non-polymers3,49618
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Glutamate dehydrogenase 1, mitochondrial / GDH 1


Mass: 54880.406 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: liver
References: UniProt: P00366, glutamate dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-A1JTK / 2-azanyl-1,3-benzothiazole-6-carboxylic acid


Mass: 194.210 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C8H6N2O2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: L-Glutamic Dehydrogenase 1 (GDH1) / Type: COMPLEX
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
Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: liver
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8.2
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMHEPESHEPES1
2150 mMSodium ChlorideNaCl1
35 %DMSODMSO1
40.001 %Tween-20Tween-201
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 59.98 sec. / Electron dose: 62.51 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1444
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1Gautomatch0.53particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
9PHENIXmodel refinement
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 277213 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: Other / Type: experimental model

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