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- EMDB-74581: Composite map of the bGDH di-hexamer in liganded form -

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Basic information

Entry
Database: EMDB / ID: EMD-74581
TitleComposite map of the bGDH di-hexamer in liganded form
Map dataThe composite map of dimer-of-hexameric bovine glutamate dehydrogenase in liganded form
Sample
  • Complex: Bovine glutamate dehydrogenase
    • Protein or peptide: Glutamate dehydrogenase 1, mitochondrial
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
  • Ligand: GAMMA-L-GLUTAMIC ACID
KeywordsGlutamate dehydrogenase Amino acid metabolism filament allosteric regulation / UNKNOWN FUNCTION
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 (Bovine) (domestic cattle) / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsShan Z / Lyumkis D
Funding support United States, 3 items
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, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74581.png

Downloads & links

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Map

FileDownload / File: emd_74581.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe composite map of dimer-of-hexameric bovine glutamate dehydrogenase in liganded form
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 320 pix.
= 420.864 Å		1.32 Å/pix.
x 320 pix.
= 420.864 Å		1.32 Å/pix.
x 320 pix.
= 420.864 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3152 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.09447529 - 0.67673844
Average (Standard dev.)0.004099136 (±0.014880528)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 420.86398 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Bovine glutamate dehydrogenase

EntireName: Bovine glutamate dehydrogenase
Components
  • Complex: Bovine glutamate dehydrogenase
    • Protein or peptide: Glutamate dehydrogenase 1, mitochondrial
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
  • Ligand: GAMMA-L-GLUTAMIC ACID

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Supramolecule #1: Bovine glutamate dehydrogenase

SupramoleculeName: Bovine glutamate dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (Bovine) (domestic cattle)
Molecular weightTheoretical: 780 KDa

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Macromolecule #1: Glutamate dehydrogenase 1, mitochondrial

MacromoleculeName: Glutamate dehydrogenase 1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: glutamate dehydrogenase [NAD(P)+]
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 61.593832 KDa
SequenceString: MYRYLGEALL LSRAGPAALG SASADSAALL GWARGQPAAA PQPGLVPPAR RHYSEAAADR EDDPNFFKMV EGFFDRGASI VEDKLVEDL KTRETEEQKR NRVRSILRII KPCNHVLSLS FPIRRDDGSW EVIEGYRAQH SQHRTPCKGG IRYSTDVSVD E VKALASLM ...String:
MYRYLGEALL LSRAGPAALG SASADSAALL GWARGQPAAA PQPGLVPPAR RHYSEAAADR EDDPNFFKMV EGFFDRGASI VEDKLVEDL KTRETEEQKR NRVRSILRII KPCNHVLSLS FPIRRDDGSW EVIEGYRAQH SQHRTPCKGG IRYSTDVSVD E VKALASLM TYKCAVVDVP FGGAKAGVKI NPKNYTDNEL EKITRRFTME LAKKGFIGPG VDVPAPDMST GEREMSWIAD TY ASTIGHY DINAHACVTG KPISQGGIHG RISATGRGVF HGIENFINEA SYMSILGMTP GFGDKTFVVQ GFGNVGLHSM RYL HRFGAK CITVGESDGS IWNPDGIDPK ELEDFKLQHG TILGFPKAKI YEGSILEVDC DILIPAASEK QLTKSNAPRV KAKI IAEGA NGPTTPEADK IFLERNIMVI PDLYLNAGGV TVSYFEWLNN LNHVSYGRLT FKYERDSNYH LLMSVQESLE RKFGK HGGT IPIVPTAEFQ DRISGASEKD IVHSGLAYTM ERSARQIMRT AMKYNLGLDL RTAAYVNAIE KVFRVYNEAG VTFT

UniProtKB: Glutamate dehydrogenase 1, mitochondrial

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Macromolecule #2: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #3: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

MacromoleculeName: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 24 / Formula: NAI
Molecular weightTheoretical: 665.441 Da
Chemical component information

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

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Macromolecule #4: GAMMA-L-GLUTAMIC ACID

MacromoleculeName: GAMMA-L-GLUTAMIC ACID / type: ligand / ID: 4 / Number of copies: 6 / Formula: GGL
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GGL:
GAMMA-L-GLUTAMIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 44.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: An atomic bGDH model derived from AlphaFold3 prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software - Name: UCSF Chimera / Number images used: 97554
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9zqt:
Composite map of the bGDH di-hexamer in liganded form

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