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- EMDB-35574: Filament interface structure of GAC with phosphate -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-35574
TitleFilament interface structure of GAC with phosphate
Map data
Sample
  • Complex: GAC filament with phosphate
    • Protein or peptide: Glutaminase kidney isoform, mitochondrial
  • Ligand: PHOSPHATE ION
KeywordsGlutaminase / phosphate / filament / PROTEIN FIBRIL / HYDROLASE
Function / homology
Function and homology information


glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes ...glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes / chemical synaptic transmission / protein homotetramerization / mitochondrial matrix / synapse / mitochondrion / cytosol
Similarity search - Function
Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Beta-lactamase/transpeptidase-like / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGuo CJ / Liu JL
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2024
Title: Structural basis for activation and filamentation of glutaminase.
Authors: Chen-Jun Guo / Zi-Xuan Wang / Ji-Long Liu /
History
DepositionMar 6, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35574.png

Downloads & links

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Map

FileDownload / File: emd_35574.map.gz / Format: CCP4 / Size: 5.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 115 pix.
= 121.9 Å		1.06 Å/pix.
x 161 pix.
= 170.66 Å		1.06 Å/pix.
x 83 pix.
= 87.98 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-3.2687817 - 3.8937457
Average (Standard dev.)-0.000000000000693 (±0.28895548)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin205943
Dimensions16183115
Spacing11516183
CellA: 121.899994 Å / B: 170.65999 Å / C: 87.979996 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35574_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35574_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35574_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GAC filament with phosphate

EntireName: GAC filament with phosphate
Components
  • Complex: GAC filament with phosphate
    • Protein or peptide: Glutaminase kidney isoform, mitochondrial
  • Ligand: PHOSPHATE ION

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Supramolecule #1: GAC filament with phosphate

SupramoleculeName: GAC filament with phosphate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glutaminase kidney isoform, mitochondrial

MacromoleculeName: Glutaminase kidney isoform, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: glutaminase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.083738 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: LVASGENKIK QGLLPSLEDL LFYTIAEGQE KIPVHKFITA LKSTGLRTSD PRLKECMDML RLTLQTTSDG VMLDKDLFKK CVQSNIVLL TQAFRRKFVI PDFMSFTSHI DELYESAKKQ SGGKVADYIP QLAKFSPDLW GVSVCTVDGQ RHSTGDTKVP F CLQSCVKP ...String:
LVASGENKIK QGLLPSLEDL LFYTIAEGQE KIPVHKFITA LKSTGLRTSD PRLKECMDML RLTLQTTSDG VMLDKDLFKK CVQSNIVLL TQAFRRKFVI PDFMSFTSHI DELYESAKKQ SGGKVADYIP QLAKFSPDLW GVSVCTVDGQ RHSTGDTKVP F CLQSCVKP LKYAIAVNDL GTEYVHRYVG KEPSGLRFNK LFLNEDDKPH NPMVNAGAIV VTSLIKQGVN NAEKFDYVMQ FL NKMAGNE YVGFSNATFQ SERESGDRNF AIGYYLKEKK CFPEGTDMVG ILDFYFQLCS IEVTCESASV MAATLANGGF CPI TGERVL SPEAVRNTLS LMHSCGMYDF SGQFAFHVGL PAKSGVAGGI LLVVPNVMGM MCWSPPLDKM GNSVKGIHFC HDLV SLCNF HNYDNLRHFA KKLDPRREGG DQRHSFGPLD YESLQQELAL KETVWKKVSP ESNEDISTTV VYRMESLGEK S

UniProtKB: Glutaminase kidney isoform, mitochondrial

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Macromolecule #2: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3vp1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 321414
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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