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- EMDB-40764: Human asparagine synthetase (apo-ASNS) -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-40764
TitleHuman asparagine synthetase (apo-ASNS)
Map dataSharpened ASNS EM map
Sample
  • Organelle or cellular component: human asparagine synthetase dimer form
    • Protein or peptide: Asparagine synthetase [glutamine-hydrolyzing]
Keywordsasparagine / aspartic acid / glutamine / ammonia / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


asparagine synthase (glutamine-hydrolysing) / L-asparagine biosynthetic process / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / Response of EIF2AK1 (HRI) to heme deficiency / Aspartate and asparagine metabolism / ATF4 activates genes in response to endoplasmic reticulum stress / glutamine metabolic process / Response of EIF2AK4 (GCN2) to amino acid deficiency / cellular response to glucose starvation ...asparagine synthase (glutamine-hydrolysing) / L-asparagine biosynthetic process / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / Response of EIF2AK1 (HRI) to heme deficiency / Aspartate and asparagine metabolism / ATF4 activates genes in response to endoplasmic reticulum stress / glutamine metabolic process / Response of EIF2AK4 (GCN2) to amino acid deficiency / cellular response to glucose starvation / positive regulation of mitotic cell cycle / negative regulation of apoptotic process / ATP binding / cytosol
Similarity search - Function
Asparagine synthase, glutamine-hydrolyzing / Asparagine synthase, N-terminal domain / : / Glutamine amidotransferase domain / Asparagine synthase / Asparagine synthase / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Nucleophile aminohydrolases, N-terminal / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Asparagine synthetase [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCoricello A / Zhu W / Lupia A / Gratteri C / Vos M / Chaptal V / Alcaro S / Takagi Y / Richards N
Funding support United States, France, United Kingdom, European Union, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM111695 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD028723 United States
Centre National de la Recherche Scientifique (CNRS)ANR-19-CE11-0023-01 France
Biotechnology and Biological Sciences Research Council (BBSRC)P/0118017/1 United Kingdom
European CommissionFESR FSE 2014- 2020European Union
CitationJournal: To Be Published
Title: Human asparagine synthetase (apo-ASNS)
Authors: Takagi Y
History
DepositionMay 12, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40764.png

Downloads & links

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Map

FileDownload / File: emd_40764.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened ASNS EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.02320113 - 2.1356351
Average (Standard dev.)0.0015063072 (±0.02873001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: ASNS half map B

Fileemd_40764_half_map_1.map
AnnotationASNS half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ASNS half map A

Fileemd_40764_half_map_2.map
AnnotationASNS half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human asparagine synthetase dimer form

EntireName: human asparagine synthetase dimer form
Components
  • Organelle or cellular component: human asparagine synthetase dimer form
    • Protein or peptide: Asparagine synthetase [glutamine-hydrolyzing]

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Supramolecule #1: human asparagine synthetase dimer form

SupramoleculeName: human asparagine synthetase dimer form / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 133 KDa

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Macromolecule #1: Asparagine synthetase [glutamine-hydrolyzing]

MacromoleculeName: Asparagine synthetase [glutamine-hydrolyzing] / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: asparagine synthase (glutamine-hydrolysing)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.324613 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: CGIWALFGSD DCLSVQCLSA MKIAHRGPDA FRFENVNGYT NCCFGFHRLA VVDPLFGMQP IRVKKYPYLW LCYNGEIYNH KKMQQHFEF EYQTKVDGEI ILHLYDKGGI EQTICMLDGV FAFVLLDTAN KKVFLGRDTY GVRPLFKAMT EDGFLAVCSE A KGLVTLKH ...String:
CGIWALFGSD DCLSVQCLSA MKIAHRGPDA FRFENVNGYT NCCFGFHRLA VVDPLFGMQP IRVKKYPYLW LCYNGEIYNH KKMQQHFEF EYQTKVDGEI ILHLYDKGGI EQTICMLDGV FAFVLLDTAN KKVFLGRDTY GVRPLFKAMT EDGFLAVCSE A KGLVTLKH SATPFLKVEP FLPGHYEVLD LKPNGKVASV EMVKYHHCRD VPLHALYDNV EKLFPGFEIE TVKNNLRILF NN AVKKRLM TDRRIGCLLS GGLDSSLVAA TLLKQLKEAQ VQYPLQTFAI GMEDSPDLLA ARKVADHIGS EHYEVLFNSE EGI QALDEV IFSLETYDIT TVRASVGMYL ISKYIRKNTD SVVIFSGEGS DELTQGYIYF HKAPSPEKAE EESERLLREL YLFD VLRAD RTTAAHGLEL RVPFLDHRFS SYYLSLPPEM RIPKNGIEKH LLRETFEDSN LIPKEILWRP KEAFSDGITS VKNSW FKIL QEYVEHQVDD AMMANAAQKF PFNTPKTKEG YYYRQVFERH YPGRADWLSH YWMPKWINAT DPSARTLTHY KSAVKA

UniProtKB: Asparagine synthetase [glutamine-hydrolyzing]

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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: 8
Details: 25 mM Tris-HCl, pH 8.0, containing 250 mM NaCl and 5 mM DTT.
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Details9

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm

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Image processing

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

6gq3

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47929
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6gq3


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8sue:
Human asparagine synthetase (apo-ASNS)

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