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- PDB-9zqs: Mono-hexameric bGDH map in apo form -

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Basic information

Entry
Database: PDB / ID: 9zqs
TitleMono-hexameric bGDH map in apo form
ComponentsGlutamate dehydrogenase 1, mitochondrial
KeywordsUNKNOWN FUNCTION / Glutamate dehydrogenase Amino acid metabolism filament allosteric regulation
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-glutamate catabolic process / L-glutamine metabolic process / mitochondrial inner membrane / GTP binding / endoplasmic reticulum ...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-glutamate catabolic process / L-glutamine metabolic process / mitochondrial inner membrane / GTP binding / endoplasmic reticulum / mitochondrion / ATP binding / 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: 2.52 Å
AuthorsShan, Z. / Lyumkis, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1934291 United States
National Science Foundation (NSF, United States)DBI-2018942 United States
National Science Foundation (NSF, United States)MCB 2048095 United States
CitationJournal: bioRxiv / Year: 2026
Title: Structural Mechanism of Filamentation Induced Dampening of GTP Inhibition of Glutamate Dehydrogenase.
Authors: Zelin Shan / Noura I Darwish / Andres Rivero-Gamez / Timothy S Strutzenberg / Dmitry Lyumkis / Nancy C Horton /
Abstract: Glutamate dehydrogenase (GDH) is a highly regulated key enzyme that catalyzes the reversible oxidative deamination of glutamate to -ketoglutarate, positioning it at a critical hub linking amino acid ...Glutamate dehydrogenase (GDH) is a highly regulated key enzyme that catalyzes the reversible oxidative deamination of glutamate to -ketoglutarate, positioning it at a critical hub linking amino acid catabolism to energy production while supplying ammonia for urea synthesis and other nitrogen pathways. Early investigations have shown that bovine GDH (bGDH), which shares 98% sequence identity with its human homolog, assembles into polymeric filaments with altered allosteric responses. Filamentation has only relatively recently been appreciated as a widespread mechanism of enzyme regulation, prompting a reevaluation of these early observations in GDH. Here, we use high-resolution cryogenic electron microscopy (cryo-EM) to show that bGDH hexamers assemble via reciprocal "antenna" interactions that oppose the conformational changes associated with GTP inhibition, revealing how filamentation reshapes GDH allostery and with implications for the treatment of human disease.
History
DepositionDec 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / 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


Theoretical massNumber of molelcules
Total (without water)369,5636
Polymers369,5636
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 61593.832 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P00366, glutamate dehydrogenase [NAD(P)+]
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
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: Bovine glutamate dehydrogenase / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.78 MDa / Experimental value: NO
Source (natural)Organism: Bos taurus (Bovine) (domestic cattle)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 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 defocus max: 3000 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 40.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
9cryoSPARCinitial Euler assignment
12cryoSPARC4.2.13D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132297 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 2.52 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00223574
ELECTRON MICROSCOPYf_angle_d0.37131818
ELECTRON MICROSCOPYf_dihedral_angle_d9.1488784
ELECTRON MICROSCOPYf_chiral_restr0.043456
ELECTRON MICROSCOPYf_plane_restr0.0034140

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