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- PDB-8sk8: human liver mitochondrial Glutamate dehydrogenase 1 -

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Basic information

Entry
Database: PDB / ID: 8sk8
Titlehuman liver mitochondrial Glutamate dehydrogenase 1
ComponentsGlutamate dehydrogenase 1, mitochondrial
KeywordsOXIDOREDUCTASE / human / liver / mitochondrial / Glutamate dehydrogenase 1
Function / homology
Function and homology information


glutamate dehydrogenase [NAD(P)+] activity / L-leucine binding / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / Glutamate and glutamine metabolism / L-glutamate catabolic process / glutamine metabolic process ...glutamate dehydrogenase [NAD(P)+] activity / L-leucine binding / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / Glutamate and glutamine metabolism / L-glutamate catabolic process / glutamine metabolic process / NAD+ binding / substantia nigra development / Mitochondrial protein degradation / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / ADP binding / mitochondrial matrix / GTP binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / ATP binding / cytoplasm
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 speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.31 Å
AuthorsZhang, Z. / Tringides, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI145069 United States
CitationJournal: Mol Cell Proteomics / Year: 2023
Title: High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology.
Authors: Zhemin Zhang / Marios L Tringides / Christopher E Morgan / Masaru Miyagi / Jason A Mears / Charles L Hoppel / Edward W Yu /
Abstract: The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of ...The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of single particle cryo-EM to identify multiple proteins from three enriched heterogeneous fractions prepared from human liver mitochondrial lysate. We simultaneously identify and solve high-resolution structures of nine essential mitochondrial enzymes with key metabolic functions, including fatty acid catabolism, reactive oxidative species clearance, and amino acid metabolism. Our methodology also identified multiple distinct members of the acyl-CoA dehydrogenase family. This work highlights the potential of cryo-EM to explore tissue proteomics at the atomic level.
History
DepositionApr 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.0Feb 21, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 21, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 21, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 21, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 21, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 21, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)368,8846
Polymers368,8846
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 61480.746 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P00367, glutamate dehydrogenase [NAD(P)+]
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: Glutamate dehydrogenase 1 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62508 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00423424
ELECTRON MICROSCOPYf_angle_d0.43231656
ELECTRON MICROSCOPYf_dihedral_angle_d10.3128598
ELECTRON MICROSCOPYf_chiral_restr0.0413444
ELECTRON MICROSCOPYf_plane_restr0.0044128

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