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- EMDB-4761: Escherichia coli AGPase in complex with AMP. -

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Basic information

Entry
Database: EMDB / ID: EMD-4761
TitleEscherichia coli AGPase in complex with AMP.
Map dataSharp Full Map D2 single particle reconstruction of bacterial protein with its inhibitor (corresponds to image)
Sample
  • Complex: ADP.glucose pyrophosphorylase in complex with the inhibitor AMP
    • Protein or peptide: Glucose-1-phosphate adenylyltransferase
  • Ligand: ADENOSINE MONOPHOSPHATE
KeywordsADP-glucose pyrophosphorilase Complex with AMP inhibitor / TRANSFERASE
Function / homology
Function and homology information


glucose-1-phosphate adenylyltransferase complex / glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / glycogen biosynthetic process / AMP binding / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding
Similarity search - Function
Glucose-1-phosphate adenylyltransferase GlgC, bacterial / ADP-glucose pyrophosphorylase, conserved site / Glucose-1-phosphate adenylyltransferase / ADP-glucose pyrophosphorylase signature 1. / ADP-glucose pyrophosphorylase signature 2. / ADP-glucose pyrophosphorylase signature 3. / : / GlmU-like, C-terminal hexapeptide / Nucleotidyl transferase domain / Nucleotidyl transferase ...Glucose-1-phosphate adenylyltransferase GlgC, bacterial / ADP-glucose pyrophosphorylase, conserved site / Glucose-1-phosphate adenylyltransferase / ADP-glucose pyrophosphorylase signature 1. / ADP-glucose pyrophosphorylase signature 2. / ADP-glucose pyrophosphorylase signature 3. / : / GlmU-like, C-terminal hexapeptide / Nucleotidyl transferase domain / Nucleotidyl transferase / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Glucose-1-phosphate adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsCifuente JO / Comino N
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and Competitiveness Spain
CitationJournal: Biorxiv / Year: 2020
Title: The allosteric control mechanism of bacterial glycogen biosynthesis disclosed by cryoEM
Authors: Cifuente JO / Comino N / D'Angelo C / Marina A / Gil-Carton D / Albesa-Jove D / Guerin ME
History
DepositionApr 2, 2019-
Header (metadata) releaseFeb 5, 2020-
Map releaseFeb 5, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.31
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.31
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6r8u
  • Surface level: 0.31
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4761.png

Downloads & links

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Map

FileDownload / File: emd_4761.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharp Full Map D2 single particle reconstruction of bacterial protein with its inhibitor (corresponds to image)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 200 pix.
= 209.4 Å		1.05 Å/pix.
x 200 pix.
= 209.4 Å		1.05 Å/pix.
x 200 pix.
= 209.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31 / Movie #1: 0.31
Minimum - Maximum-2.1101058 - 3.3964782
Average (Standard dev.)0.00064358494 (±0.1359254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 209.40001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0471.0471.047
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z209.400209.400209.400
α/β/γ90.00090.00090.000
start NX/NY/NZ29921935
NX/NY/NZ271234450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-2.1103.3960.001

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Supplemental data

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Additional map: Full Map D2 single particle reconstruction of bacterial...

Fileemd_4761_additional_1.map
AnnotationFull Map D2 single particle reconstruction of bacterial protein with its inhibitor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: First Half Map D2 single particle reconstruction of...

Fileemd_4761_additional_2.map
AnnotationFirst Half Map D2 single particle reconstruction of bacterial protein with its inhibitor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Second Half Map D2 single particle reconstruction of...

Fileemd_4761_additional_3.map
AnnotationSecond Half Map D2 single particle reconstruction of bacterial protein with its inhibitor
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ADP.glucose pyrophosphorylase in complex with the inhibitor AMP

EntireName: ADP.glucose pyrophosphorylase in complex with the inhibitor AMP
Components
  • Complex: ADP.glucose pyrophosphorylase in complex with the inhibitor AMP
    • Protein or peptide: Glucose-1-phosphate adenylyltransferase
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: ADP.glucose pyrophosphorylase in complex with the inhibitor AMP

SupramoleculeName: ADP.glucose pyrophosphorylase in complex with the inhibitor AMP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Homotetrameric enzyme
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 194 KDa

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Macromolecule #1: Glucose-1-phosphate adenylyltransferase

MacromoleculeName: Glucose-1-phosphate adenylyltransferase / type: protein_or_peptide / ID: 1 / Details: Complex with AMP / Number of copies: 4 / Enantiomer: LEVO / EC number: glucose-1-phosphate adenylyltransferase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 48.75859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVSLEKNDHL MLARQLPLKS VALILAGGRG TRLKDLTNKR AKPAVHFGGK FRIIDFALSN CINSGIRRMG VITQYQSHTL VQHIQRGWS FFNEEMNEFV DLLPAQQRMK GENWYRGTAD AVTQNLDIIR RYKAEYVVIL AGDHIYKQDY SRMLIDHVEK G ARCTVACM ...String:
MVSLEKNDHL MLARQLPLKS VALILAGGRG TRLKDLTNKR AKPAVHFGGK FRIIDFALSN CINSGIRRMG VITQYQSHTL VQHIQRGWS FFNEEMNEFV DLLPAQQRMK GENWYRGTAD AVTQNLDIIR RYKAEYVVIL AGDHIYKQDY SRMLIDHVEK G ARCTVACM PVPIEEASAF GVMAVDENDK IIEFVEKPAN PPSMPNDPSK SLASMGIYVF DADYLYELLE EDDRDENSSH DF GKDLIPK ITEAGLAYAH PFPLSCVQSD PDAEPYWRDV GTLEAYWKAN LDLASVVPEL DMYDRNWPIR TYNESLPPAK FVQ DRSGSH GMTLNSLVSG GCVISGSVVV QSVLFSRVRV NSFCNIDSAV LLPEVWVGRS CRLRRCVIDR ACVIPEGMVI GENA EEDAR RFYRSEEGIV LVTREMLRKL GHKQER

UniProtKB: Glucose-1-phosphate adenylyltransferase

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Macromolecule #2: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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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

Concentration0.35 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
50.0 mMTris/Cl
100.0 mMNaCl
0.05 mMAdenosine Mono Phosphate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK II
DetailsSample with single particles and some linear chains of particles

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMax: 80.0 K
DetailsTitan Krios I - Ebic - Diamond Light Source
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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:

5l6s


Details: Calculated density map at 35A resolution
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2) / Software - details: Non-uniform refinement / Number images used: 94769
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5l6v


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6r8u:
Escherichia coli AGPase in complex with AMP.

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