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- EMDB-60346: EcGK bundle at APO state. (CASP target) -

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Basic information

Entry
Database: EMDB / ID: EMD-60346
TitleEcGK bundle at APO state. (CASP target)
Map data
Sample
  • Complex: EcGK at APO state
    • Protein or peptide: Glutamate 5-kinase
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 / proline biosynthetic process / phosphorylation / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding ...proline binding / glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / proline biosynthetic process / phosphorylation / 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 profile. ...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 profile. / PUA domain superfamily / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / PUA-like superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (strain K12) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.97 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
DepositionMay 30, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60346.png

Downloads & links

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Map

FileDownload / File: emd_60346.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. 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: 0.07
Minimum - Maximum-0.04766672 - 0.18304494
Average (Standard dev.)0.002073653 (±0.015879145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local filtered map

Fileemd_60346_additional_1.map
AnnotationLocal filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map with helical symmetry applied.

Fileemd_60346_additional_2.map
AnnotationMap with helical symmetry applied.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60346_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_60346_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

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Supramolecule #1: EcGK at APO state

SupramoleculeName: EcGK at APO state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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 BL21(DE3) (bacteria)
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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Experimental details

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Structure determination

Methodcryo EM
Processinghelical 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

Final reconstructionApplied symmetry - Helical parameters - Δz: 21.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 85.85 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 512330
Startup modelType of model: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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