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- EMDB-52425: CryoEM map of the large glutamate dehydrogenase composed of 180 k... -

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Basic information

Entry
Database: EMDB / ID: EMD-52425
TitleCryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. cofactor/ligand-monomer in Open tetramer.
Map data
Sample
  • Complex: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate
KeywordsLarge glutamate dehydrogenase / Tetramer / OXIDOREDUCTASE
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsLazaro M / Chamorro N / Lopez-Alonso JP / Charro D / Rasia RM / Jimenez-Oses G / Valle M / Lisa MN
Funding support Spain, 1 items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2021-124074NB-I00 Spain
CitationJournal: Protein Sci / Year: 2026
Title: Tertiary and quaternary structure remodeling by occupancy of the substrate binding pocket in a large glutamate dehydrogenase.
Authors: Melisa Lázaro / Nicolás Chamorro / Jorge P López-Alonso / Diego Charro / Rodolfo M Rasia / Gonzalo Jiménez-Osés / Mikel Valle / María-Natalia Lisa /
Abstract: Glutamate dehydrogenases (GDHs) catalyze the oxidative deamination of L-glutamate to 2-oxoglutarate using NAD(P) as a cofactor. The large type of GDHs (L-GDHs) displays a dynamic homotetrameric ...Glutamate dehydrogenases (GDHs) catalyze the oxidative deamination of L-glutamate to 2-oxoglutarate using NAD(P) as a cofactor. The large type of GDHs (L-GDHs) displays a dynamic homotetrameric architecture that alternates between open and closed states. However, the catalytic mechanism and the functional relevance of the large conformational changes in L-GDHs remain poorly understood. Here, we use cryo-EM to investigate the structure and the conformational landscape of the mycobacterial L-GDH composed of 180 kDa subunits (mL-GDH) when incubated with L-glutamate and NAD. Classification of the heterogeneous population of tetramers reveals opening-closing motions and sorting of individual subunits resolves the occupancy of the cofactor and substrate binding pockets. Cryo-EM maps show that ligand binding to the glutamate binding pocket is accompanied by structural changes in a region approximately two nanometers away from the active site, leading to the formation of a previously undetected interaction between the catalytic domains of neighboring subunits in mL-GDH closed tetrameric states. Our findings indicate that the occupancy of the substrate binding site of mL-GDH is linked to a remodeling of both the tertiary and quaternary structure of the enzyme.
History
DepositionDec 24, 2024-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52425.png

Downloads & links

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Map

FileDownload / File: emd_52425.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.6462 Å
Density
Contour LevelBy AUTHOR: 2.45
Minimum - Maximum-0.3390274 - 17.328983000000001
Average (Standard dev.)0.005302709 (±0.19953243)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions680680680
Spacing680680680
CellA=B=C: 439.41602 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52425_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52425_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52425_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis...

EntireName: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate
Components
  • Complex: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate

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Supramolecule #1: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis...

SupramoleculeName: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: MsLGDH180 Open-cofactor/ligand-monomer
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: strain ATCC 700084 / mc(2)155
Molecular weightTheoretical: 174 KDa

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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

Concentration0.125 mg/mL
BufferpH: 6.5
Component:
ConcentrationName
20.0 mMMES
300.0 mMNaCl
42.0 mMGlutamate
4.0 mMNAD
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

11606


Details: Cryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (open conformation) at 4.19 A resolution
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 33330
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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