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- EMDB-26915: Glutamate dehydrogenase 1 from human liver -

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Basic information

Entry
Database: EMDB / ID: EMD-26915
TitleGlutamate dehydrogenase 1 from human liver
Map data
Sample
  • Complex: Glutamate dehydrogenase 1
    • Protein or peptide: Glutamate dehydrogenase 1, mitochondrial
Keywordsaldehyde dehydrogenase / human liver / OXIDOREDUCTASE
Function / homology
Function and homology information


L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / Glutamate and glutamine metabolism / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / glutamate catabolic process / glutamine metabolic process ...L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / Glutamate and glutamine metabolism / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsZhang Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2023
Title: High-resolution structural-omics of human liver enzymes.
Authors: Chih-Chia Su / Meinan Lyu / Zhemin Zhang / Masaru Miyagi / Wei Huang / Derek J Taylor / Edward W Yu /
Abstract: We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined ...We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level.
History
DepositionMay 9, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26915.png

Downloads & links

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Map

FileDownload / File: emd_26915.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
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Contour LevelBy AUTHOR: 0.104
Minimum - Maximum-0.9440323 - 1.5561172
Average (Standard dev.)0.0011092664 (±0.038800374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_26915_additional_1.map
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Half map: #2

Fileemd_26915_half_map_1.map
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Half map: #1

Fileemd_26915_half_map_2.map
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Sample components

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Entire : Glutamate dehydrogenase 1

EntireName: Glutamate dehydrogenase 1
Components
  • Complex: Glutamate dehydrogenase 1
    • Protein or peptide: Glutamate dehydrogenase 1, mitochondrial

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Supramolecule #1: Glutamate dehydrogenase 1

SupramoleculeName: Glutamate dehydrogenase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glutamate dehydrogenase 1, mitochondrial

MacromoleculeName: Glutamate dehydrogenase 1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: glutamate dehydrogenase [NAD(P)+]
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.480746 KDa
SequenceString: MYRYLGEALL LSRAGPAALG SASADSAALL GWARGQPAAA PQPGLALAAR RHYSEAVADR EDDPNFFKMV EGFFDRGASI VEDKLVEDL RTRESEEQKR NRVRGILRII KPCNHVLSLS FPIRRDDGSW EVIEGYRAQH SQHRTPCKGG IRYSTDVSVD E VKALASLM ...String:
MYRYLGEALL LSRAGPAALG SASADSAALL GWARGQPAAA PQPGLALAAR RHYSEAVADR EDDPNFFKMV EGFFDRGASI VEDKLVEDL RTRESEEQKR NRVRGILRII KPCNHVLSLS FPIRRDDGSW EVIEGYRAQH SQHRTPCKGG IRYSTDVSVD E VKALASLM TYKCAVVDVP FGGAKAGVKI NPKNYTDNEL EKITRRFTME LAKKGFIGPG IDVPAPDMST GEREMSWIAD TY ASTIGHY DINAHACVTG KPISQGGIHG RISATGRGVF HGIENFINEA SYMSILGMTP GFGDKTFVVQ GFGNVGLHSM RYL HRFGAK CIAVGESDGS IWNPDGIDPK ELEDFKLQHG SILGFPKAKP YEGSILEADC DILIPAASEK QLTKSNAPRV KAKI IAEGA NGPTTPEADK IFLERNIMVI PDLYLNAGGV TVSYFEWLKN LNHVSYGRLT FKYERDSNYH LLMSVQESLE RKFGK HGGT IPIVPTAEFQ DRISGASEKD IVHSGLAYTM ERSARQIMRT AMKYNLGLDL RTAAYVNAIE KVFKVYNEAG VTFT

UniProtKB: Glutamate dehydrogenase 1, mitochondrial

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.291 µm / Nominal defocus min: 0.17 µm / Nominal magnification: 82000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 837478
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10295
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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