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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20411 | ||||||||||||
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Title | MicroED Structure of a Natural Product VFAThiaGlu | ||||||||||||
![]() | Natural Product VFAThiaGlu | ||||||||||||
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![]() | Ribosomal synthesized small peptide / MicroED / microcrystal electron diffraction / UNKNOWN FUNCTION | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | electron crystallography / cryo EM | ||||||||||||
![]() | Halaby S / Gonen T | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Use of a scaffold peptide in the biosynthesis of amino acid-derived natural products. Authors: Chi P Ting / Michael A Funk / Steve L Halaby / Zhengan Zhang / Tamir Gonen / Wilfred A van der Donk / ![]() Abstract: Genome sequencing of environmental bacteria allows identification of biosynthetic gene clusters encoding unusual combinations of enzymes that produce unknown natural products. We identified a pathway ...Genome sequencing of environmental bacteria allows identification of biosynthetic gene clusters encoding unusual combinations of enzymes that produce unknown natural products. We identified a pathway in which a ribosomally synthesized small peptide serves as a scaffold for nonribosomal peptide extension and chemical modification. Amino acids are transferred to the carboxyl terminus of the peptide through adenosine triphosphate and amino acyl-tRNA-dependent chemistry that is independent of the ribosome. Oxidative rearrangement, carboxymethylation, and proteolysis of a terminal cysteine yields an amino acid-derived small molecule. Microcrystal electron diffraction demonstrates that the resulting product is isosteric to glutamate. We show that a similar peptide extension is used during the biosynthesis of the ammosamides, which are cytotoxic pyrroloquinoline alkaloids. These results suggest an alternative paradigm for biosynthesis of amino acid-derived natural products. | ||||||||||||
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 | ![]() | 233.1 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.9 KB 11.9 KB | Display Display | ![]() |
Images | ![]() | 103.2 KB | ||
Filedesc metadata | ![]() | 4.6 KB | ||
Filedesc structureFactors | ![]() | 50.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Natural Product VFAThiaGlu | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.30188 Å / Y: 0.29938 Å / Z: 0.31947 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : VAL-PHE-ALA-ThiaGLU
Entire | Name: VAL-PHE-ALA-ThiaGLU |
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Components |
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-Supramolecule #1: VAL-PHE-ALA-ThiaGLU
Supramolecule | Name: VAL-PHE-ALA-ThiaGLU / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: YFAThiaGlu
Macromolecule | Name: YFAThiaGlu / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 482.55 Da |
Sequence | String: VFA(OV7) |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 1 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | electron crystallography |
Aggregation state | 3D array |
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Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: NITROGEN / Instrument: HOMEMADE PLUNGER |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Temperature | Min: 77.0 K / Max: 100.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 0.01 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION / Camera length: 1100 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution method: DIFFRACTION PATTERN/LAYERLINES |
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Crystallography statistics | Number intensities measured: 7590 / Number structure factors: 3047 / Fourier space coverage: 95.4 / R sym: 23.5 / R merge: 23.5 / Overall phase error: 0 / Overall phase residual: 15 / Phase error rejection criteria: 0 / High resolution: 0.9 Å / Shell - Shell ID: 1 / Shell - High resolution: 0.9 Å / Shell - Low resolution: 0.93 Å / Shell - Number structure factors: 642 / Shell - Phase residual: 15 / Shell - Fourier space coverage: 92.8 / Shell - Multiplicity: 2.25 |
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 3.746 |
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Output model | ![]() PDB-6po6: |