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- EMDB-20411: MicroED Structure of a Natural Product VFAThiaGlu -

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Basic information

Entry
Database: EMDB / ID: EMD-20411
TitleMicroED Structure of a Natural Product VFAThiaGlu
Map dataNatural Product VFAThiaGlu
Sample
  • Complex: VAL-PHE-ALA-ThiaGLU
    • Protein or peptide: YFAThiaGlu
  • Ligand: water
KeywordsRibosomal synthesized small peptide / MicroED / microcrystal electron diffraction / UNKNOWN FUNCTION
Biological speciesPseudomonas syringae (bacteria)
Methodelectron crystallography / cryo EM
AuthorsHalaby S / Gonen T
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R37 GM058822 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)F32 GM129944 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)F32 GM120868 United States
CitationJournal: Science / Year: 2019
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
DepositionJul 3, 2019-
Header (metadata) releaseAug 7, 2019-
Map releaseAug 7, 2019-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.47628
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.47628
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6po6
  • Surface level: 0.47628
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6po6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20411.png

Downloads & links

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Map

FileDownload / File: emd_20411.map.gz / Format: CCP4 / Size: 1004.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNatural Product VFAThiaGlu
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
0.3 Å/pix.
x 51 pix.
= 9.58 Å		0.3 Å/pix.
x 63 pix.
= 9.66 Å		0.32 Å/pix.
x 80 pix.
= 12.14 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.30188 Å / Y: 0.29938 Å / Z: 0.31947 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.47628 / Movie #1: 0.47628
Minimum - Maximum-0.40235433 - 3.662926
Average (Standard dev.)-0.005296943 (±0.3175154)
SymmetrySpace group: 4
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-15-23-9
Dimensions638051
Spacing323238
CellA: 9.66 Å / B: 9.58 Å / C: 12.14 Å
α: 90.0 ° / β: 93.999 ° / γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.3018750.2993750.31947368421053
M x/y/z323238
origin x/y/z0.0000.0000.000
length x/y/z9.6609.58012.140
α/β/γ90.00093.99990.000
start NX/NY/NZ-15-9-23
NX/NY/NZ635180
MAP C/R/S312
start NC/NR/NS-23-15-9
NC/NR/NS806351
D min/max/mean-0.4023.663-0.005

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Supplemental data

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Sample components

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Entire : VAL-PHE-ALA-ThiaGLU

EntireName: VAL-PHE-ALA-ThiaGLU
Components
  • Complex: VAL-PHE-ALA-ThiaGLU
    • Protein or peptide: YFAThiaGlu
  • Ligand: water

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Supramolecule #1: VAL-PHE-ALA-ThiaGLU

SupramoleculeName: VAL-PHE-ALA-ThiaGLU / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas syringae (bacteria)

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Macromolecule #1: YFAThiaGlu

MacromoleculeName: YFAThiaGlu / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas syringae (bacteria)
Molecular weightTheoretical: 482.55 Da
SequenceString:
VFA(OV7)

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: NITROGEN / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Camera length: 1100 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 77.0 K / Max: 100.0 K
Image recordingFilm 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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Crystallography statisticsNumber 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
Final reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 3.746
Output model

PDB-6po6:
MicroED Structure of a Natural Product VFAThiaGlu

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