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- EMDB-60397: EcGK filament at APO state. (CASP target) -

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Basic information

Entry
Database: EMDB / ID: EMD-60397
TitleEcGK filament at APO state. (CASP target)
Map data
Sample
  • Complex: EcGK at APO state.
    • Protein or peptide: Glutamate 5-kinase
  • Ligand: water
KeywordsTransferase / Proline biosynthesis / amino acid kinase
Function / homology
Function and homology information


proline binding / glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / : / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Glutamate 5-kinase / Glutamate-5-kinase domain / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / PUA domain / Glutamate/acetylglutamate kinase / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain superfamily ...Glutamate 5-kinase / Glutamate-5-kinase domain / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / PUA domain / Glutamate/acetylglutamate kinase / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain superfamily / PUA domain profile. / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / PUA-like superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsZhang T / Leng Q / Liu LJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: EcGPR tetramer with catalytic intermediates
Authors: Zhang T / Leng Q / Liu LJ
History
DepositionJun 4, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60397.png

Downloads & links

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Map

FileDownload / File: emd_60397.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.071780965 - 0.2347178
Average (Standard dev.)0.0012352415 (±0.012708257)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local filtered map

Fileemd_60397_additional_1.map
AnnotationLocal filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60397_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60397_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 : EcGK at APO state.

EntireName: EcGK at APO state.
Components
  • Complex: EcGK at APO state.
    • Protein or peptide: Glutamate 5-kinase
  • Ligand: water

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Supramolecule #1: EcGK at APO state.

SupramoleculeName: EcGK at APO state. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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Macromolecule #1: Glutamate 5-kinase

MacromoleculeName: Glutamate 5-kinase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: glutamate 5-kinase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 39.103457 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDSQTLVVK LGTSVLTGGS RRLNRAHIVE LVRQCAQLHA AGHRIVIVTS GAIAAGREHL GYPELPATIA SKQLLAAVGQ SRLIQLWEQ LFSIYGIHVG QMLLTRADME DRERFLNARD TLRALLDNNI VPVINENDAV ATAEIKVGDN DNLSALAAIL A GADKLLLL ...String:
MSDSQTLVVK LGTSVLTGGS RRLNRAHIVE LVRQCAQLHA AGHRIVIVTS GAIAAGREHL GYPELPATIA SKQLLAAVGQ SRLIQLWEQ LFSIYGIHVG QMLLTRADME DRERFLNARD TLRALLDNNI VPVINENDAV ATAEIKVGDN DNLSALAAIL A GADKLLLL TDQKGLYTAD PRSNPQAELI KDVYGIDDAL RAIAGDSVSG LGTGGMSTKL QAADVACRAG IDTIIAAGSK PG VIGDVME GISVGTLFHA QATPLENRKR WIFGAPPAGE ITVDEGATAA ILERGSSLLP KGIKSVTGNF SRGEVIRICN LEG RDIAHG VSRYNSDALR RIAGHHSQEI DAILGYEYGP VAVHRDDMIT R

UniProtKB: Glutamate 5-kinase

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 865 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

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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: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 337634
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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