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- EMDB-60295: EcGPR tetramer with catalytic intermediates -

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Basic information

Entry
Database: EMDB / ID: EMD-60295
TitleEcGPR tetramer with catalytic intermediates
Map data
Sample
  • Complex: EcGPR incubated with upstream enzyme GK and substrates ATP, glutamate, and NAPDH.
    • Protein or peptide: Gamma-glutamyl phosphate reductase
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: (2~{S})-2-azanyl-5-oxidanylidene-5-phosphonooxy-pentanoic acid
  • Ligand: water
KeywordsOxidoreductase / Proline biosynthesis
Function / homology
Function and homology information


glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / L-proline biosynthetic process / proline biosynthetic process / NADP binding / identical protein binding / cytosol
Similarity search - Function
Glutamate-5-semialdehyde dehydrogenase / GPR domain / Gamma-glutamyl phosphate reductase GPR, conserved site / Gamma-glutamyl phosphate reductase signature. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Gamma-glutamyl phosphate reductase
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 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 28, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60295.png

Downloads & links

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Map

FileDownload / File: emd_60295.map.gz / Format: CCP4 / Size: 40.6 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 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 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: 0.03
Minimum - Maximum-0.105381966 - 0.21923885
Average (Standard dev.)0.00044774744 (±0.008185262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 233.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60295_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local filtered map.

Fileemd_60295_additional_1.map
AnnotationLocal filtered map.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60295_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_60295_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 : EcGPR incubated with upstream enzyme GK and substrates ATP, gluta...

EntireName: EcGPR incubated with upstream enzyme GK and substrates ATP, glutamate, and NAPDH.
Components
  • Complex: EcGPR incubated with upstream enzyme GK and substrates ATP, glutamate, and NAPDH.
    • Protein or peptide: Gamma-glutamyl phosphate reductase
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: (2~{S})-2-azanyl-5-oxidanylidene-5-phosphonooxy-pentanoic acid
  • Ligand: water

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Supramolecule #1: EcGPR incubated with upstream enzyme GK and substrates ATP, gluta...

SupramoleculeName: EcGPR incubated with upstream enzyme GK and substrates ATP, glutamate, and NAPDH.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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Macromolecule #1: Gamma-glutamyl phosphate reductase

MacromoleculeName: Gamma-glutamyl phosphate reductase / type: protein_or_peptide / ID: 1 / Details: EcGPR with C-terminal 6-His tag. / Number of copies: 4 / Enantiomer: LEVO / EC number: glutamate-5-semialdehyde dehydrogenase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 45.509812 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLEQMGIAAK QASYKLAQLS SREKNRVLEK IADELEAQSE IILNANAQDV ADARANGLSE AMLDRLALTP ARLKGIADDV RQVCNLADP VGQVIDGGVL DSGLRLERRR VPLGVIGVIY EARPNVTVDV ASLCLKTGNA VILRGGKETC RTNAATVAVI Q DALKSCGL ...String:
MLEQMGIAAK QASYKLAQLS SREKNRVLEK IADELEAQSE IILNANAQDV ADARANGLSE AMLDRLALTP ARLKGIADDV RQVCNLADP VGQVIDGGVL DSGLRLERRR VPLGVIGVIY EARPNVTVDV ASLCLKTGNA VILRGGKETC RTNAATVAVI Q DALKSCGL PAGAVQAIDN PDRALVSEML RMDKYIDMLI PRGGAGLHKL CREQSTIPVI TGGIGVCHIY VDESVEIAEA LK VIVNAKT QRPSTCNTVE TLLVNKNIAD SFLPALSKQM AESGVTLHAD AAALAQLQAG PAKVVAVKAE EYDDEFLSLD LNV KIVSDL DDAIAHIREH GTQHSDAILT RDMRNAQRFV NEVDSSAVYV NASTRFTDGG QFGLGAEVAV STQKLHARGP MGLE ALTTY KWIGIGDYTI RAHHHHHH

UniProtKB: Gamma-glutamyl phosphate reductase

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Macromolecule #2: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Macromolecule #3: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #4: (2~{S})-2-azanyl-5-oxidanylidene-5-phosphonooxy-pentanoic acid

MacromoleculeName: (2~{S})-2-azanyl-5-oxidanylidene-5-phosphonooxy-pentanoic acid
type: ligand / ID: 4 / Details: EcGPR with C-terminal 6-His tag. / Number of copies: 4 / Formula: VHF
Molecular weightTheoretical: 227.109 Da
Chemical component information

ChemComp-VHF:
(2~{S})-2-azanyl-5-oxidanylidene-5-phosphonooxy-pentanoic acid

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 4 / 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

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 185467
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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