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- PDB-9huy: CryoEM map of the large glutamate dehydrogenase composed of 180 k... -

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Basic information

Entry
Database: PDB / ID: 9huy
TitleCryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. Closed1 tetramer.
ComponentsNAD-specific glutamate dehydrogenase
KeywordsOXIDOREDUCTASE / Large glutamate dehydrogenase / Tetramer
Function / homology
Function and homology information


glutamate dehydrogenase / L-glutamate dehydrogenase (NAD+) activity / L-glutamate catabolic process / L-aspartate:2-oxoglutarate aminotransferase activity
Similarity search - Function
NAD-glutamate dehydrogenase, bacteria / Bacterial NAD-glutamate dehydrogenase, N-terminal / NAD-glutamate dehydrogenase / : / : / : / : / : / : / Bacterial NAD-glutamate dehydrogenase, catalytic domain ...NAD-glutamate dehydrogenase, bacteria / Bacterial NAD-glutamate dehydrogenase, N-terminal / NAD-glutamate dehydrogenase / : / : / : / : / : / : / Bacterial NAD-glutamate dehydrogenase, catalytic domain / Glutamate dehydrogenase, helical motif 1 / Glutamate dehydrogenase, C-terminal / Glutamate dehydrogenase, ACT1 domain / Glutamate dehydrogenase, ACT2 domain / Glutamate dehydrogenase, ACT3 domain / Glutamate dehydrogenase, helical motif 3 / Glutamate dehydrogenase, helical motif 2 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-specific glutamate dehydrogenase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsLazaro, M. / Chamorro, N. / Lopez-Alonso, J.P. / Charro, D. / Rasia, R.M. / Jimenez-Oses, G. / Valle, M. / Lisa, M.N.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2021-124074NB-I00 Spain
CitationJournal: To Be Published
Title: Tertiary and quaternary structure remodeling by occupancy of the substrate binding pocket in a large glutamate dehydrogenase
Authors: Lazaro, M. / Chamorro, N. / Lopez-Alonso, J.P. / Charro, D. / Rasia, R.M. / Jimenez-Oses, G. / Valle, M. / Lisa, M.N.
History
DepositionDec 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 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: NAD-specific glutamate dehydrogenase
B: NAD-specific glutamate dehydrogenase
C: NAD-specific glutamate dehydrogenase
D: NAD-specific glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)708,0218
Polymers705,3674
Non-polymers2,6544
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
NAD-specific glutamate dehydrogenase / NAD-GDH / NAD(+)-dependent glutamate dehydrogenase


Mass: 176341.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: gdh, MSMEG_4699, MSMEI_4582 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0R1C2, glutamate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
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: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate
Type: COMPLEX / Details: MsLGDH180 tetramer in the closed1 conformation / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.174 MDa / Experimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: strain ATCC 700084 / mc(2)155
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameBuffer-ID
120 mMMES1
2300 mMNaCl1
342 mMGlutamate1
44 mMNAD1
SpecimenConc.: 0.125 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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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: 130000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4.01particle selection
2PHENIX1.21.1_5286model refinement
5RELIONCTF correction
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45998 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
RefinementCross valid method: NONE

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