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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4761 | |||||||||
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Title | Escherichia coli AGPase in complex with AMP. | |||||||||
![]() | Sharp Full Map D2 single particle reconstruction of bacterial protein with its inhibitor (corresponds to image) | |||||||||
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![]() | ADP-glucose pyrophosphorilase Complex with AMP inhibitor / TRANSFERASE | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Cifuente JO / Comino N | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.6 KB 19.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.3 KB | Display | ![]() |
Images | ![]() | 117.8 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() ![]() | 15 MB 28.2 MB 28.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 530.8 KB | Display | ![]() |
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Full document | ![]() | 530.4 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r8uMC ![]() 4754C ![]() 6r8bC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Sharp Full Map D2 single particle reconstruction of bacterial protein with its inhibitor (corresponds to image) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.047 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Full Map D2 single particle reconstruction of bacterial...
File | emd_4761_additional_1.map | ||||||||||||
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Annotation | Full Map D2 single particle reconstruction of bacterial protein with its inhibitor | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: First Half Map D2 single particle reconstruction of...
File | emd_4761_additional_2.map | ||||||||||||
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Annotation | First Half Map D2 single particle reconstruction of bacterial protein with its inhibitor | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Second Half Map D2 single particle reconstruction of...
File | emd_4761_additional_3.map | ||||||||||||
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Annotation | Second Half Map D2 single particle reconstruction of bacterial protein with its inhibitor | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : ADP.glucose pyrophosphorylase in complex with the inhibitor AMP
Entire | Name: ADP.glucose pyrophosphorylase in complex with the inhibitor AMP |
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Components |
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-Supramolecule #1: ADP.glucose pyrophosphorylase in complex with the inhibitor AMP
Supramolecule | Name: ADP.glucose pyrophosphorylase in complex with the inhibitor AMP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Homotetrameric enzyme |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 194 KDa |
-Macromolecule #1: Glucose-1-phosphate adenylyltransferase
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 48.75859 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: ADENOSINE MONOPHOSPHATE
Macromolecule | Name: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: AMP |
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Molecular weight | Theoretical: 347.221 Da |
Chemical component information | ![]() ChemComp-AMP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.35 mg/mL | ||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK II | ||||||||
Details | Sample with single particles and some linear chains of particles |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Max: 80.0 K |
Details | Titan Krios I - Ebic - Diamond Light Source |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |