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- EMDB-28639: Cryo-EM structure of glutamate dehydrogenase frozen at various te... -

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Basic information

Entry
Database: EMDB / ID: EMD-28639
TitleCryo-EM structure of glutamate dehydrogenase frozen at various temperature
Map dataThe EM map of Glutamate dehydrogenase (GDH) embedded in vitreous ice frozen at -183 celsius degree using standard procedure. The resolution of EM map is 2.7 angstrom
Sample
  • Complex: Glutamate Dehydrogenase
    • Protein or peptide: Glutamate dehydrogenase 1, mitochondrial
Keywordsglutamate dehydrogenase / GDH / Crystalline ice / LYASE
Function / homology
Function and homology information


glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamine metabolic process / mitochondrial inner membrane / GTP binding / endoplasmic reticulum ...glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / 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 (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsShi H / Wu C / Zhang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31930069 China
CitationJournal: Structure / Year: 2023
Title: Addressing compressive deformation of proteins embedded in crystalline ice.
Authors: Huigang Shi / Chunling Wu / Xinzheng Zhang /
Abstract: For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. ...For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. Whether and how crystalline ice affects single-particle cryo-EM is still unclear. Here, single-particle cryo-EM was used to analyze three-dimensional structures of various proteins and viruses embedded in crystalline ice formed at various cooling rates. Low cooling rates led to shrinkage deformation and density distortions on samples having loose structures. Higher cooling rates reduced deformations. Deformation-free proteins in crystalline ice were obtained by modifying the freezing conditions, and reconstructions from these samples revealed a marked improvement over vitreous ice. This procedure also increased the efficiency of cryo-EM structure determinations and was essential for high-resolution reconstructions.
History
DepositionOct 21, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28639.png

Downloads & links

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Map

FileDownload / File: emd_28639.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe EM map of Glutamate dehydrogenase (GDH) embedded in vitreous ice frozen at -183 celsius degree using standard procedure. The resolution of EM map is 2.7 angstrom
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.12671745 - 0.2336129
Average (Standard dev.)-0.00015022837 (±0.009649708)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28639_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: The EM map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_1.map
AnnotationThe EM map of Glutamate dehydrogenase (GDH) embedded in vitreous ice frozen at -183 celsius degree using standard procedure. The resolution of EM map is 3.1 angstrom
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The half map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_10.map
AnnotationThe half map of Glutamate dehydrogenase (GDH) embedded in crystalline ice frozen at -60 celsius degree.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The half map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_11.map
AnnotationThe half map of Glutamate dehydrogenase (GDH) embedded in crystalline ice frozen at -60 celsius degree.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The EM map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_12.map
AnnotationThe EM map of Glutamate dehydrogenase (GDH) embedded in crystalline ice frozen at -100 celsius degree. The resolution of EM map is 3.2 angstrom.
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Additional map: The half map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_13.map
AnnotationThe half map of Glutamate dehydrogenase (GDH) embedded in crystalline ice frozen at -100 celsius degree.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The EM map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_2.map
AnnotationThe EM map of Glutamate dehydrogenase (GDH) embedded in crystalline ice frozen at -183 celsius degree. The resolution of EM map is 2.5 angstrom
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The half map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_3.map
AnnotationThe half map of Glutamate dehydrogenase (GDH) embedded in crystalline ice frozen at -183 celsius degree.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The half map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_4.map
AnnotationThe half map of Glutamate dehydrogenase (GDH) embedded in crystalline ice frozen at -183 celsius degree.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The EM map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_5.map
AnnotationThe EM map of Glutamate dehydrogenase (GDH) embedded in crystalline ice frozen at -140 celsius degree. The resolution of EM map is 3.1 angstrom
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: The half map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_6.map
AnnotationThe half map of Glutamate dehydrogenase (GDH) embedded in crystalline ice frozen at -140 celsius degree.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The half map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_7.map
AnnotationThe half map of Glutamate dehydrogenase (GDH) embedded in crystalline ice frozen at -140 celsius degree.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The EM map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_8.map
AnnotationThe EM map of Glutamate dehydrogenase (GDH) embedded in crystalline ice frozen at -60 celsius degree. The resolution of EM map is 3.1 angstrom
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The EM map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_additional_9.map
AnnotationThe EM map of Glutamate dehydrogenase (GDH) embedded in crystalline ice frozen at -60 celsius degree. The resolution of EM map is 3.2 angstrom
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_half_map_1.map
AnnotationThe half map of Glutamate dehydrogenase (GDH) embedded in vitreous ice frozen at -183 celsius degree using standard procedure.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The EM map of Glutamate dehydrogenase (GDH) embedded...

Fileemd_28639_half_map_2.map
AnnotationThe EM map of Glutamate dehydrogenase (GDH) embedded in vitreous ice frozen at -183 celsius degree using standard procedure.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Glutamate Dehydrogenase

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

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Supramolecule #1: Glutamate Dehydrogenase

SupramoleculeName: Glutamate Dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (cattle)

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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: Bos taurus (cattle)
Molecular weightTheoretical: 61.60891 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 TVSYFEWLKN LNHVSYGRLT FKYERDSNYH LLMSVQESLE RKFGK HGGT IPIVPTAEFQ DRISGASEKD IVHSGLAYTM ERSARQIMRT AMKYNLGLDL RTAAYVNAIE KVFRVYNEAG 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: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 122399
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8ew0:
Cryo-EM structure of glutamate dehydrogenase frozen at various temperature

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