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- EMDB-8219: MicroED structure of thaumatin at 2.5 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-8219
TitleMicroED structure of thaumatin at 2.5 A resolution
Map dataThaumatin
Sample
  • Organelle or cellular component: Thaumatin
    • Protein or peptide: Thaumatin-1
  • Ligand: water
KeywordsSweet protein / PLANT PROTEIN
Function / homology
Function and homology information


defense response / cytoplasmic vesicle / extracellular region
Similarity search - Function
Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily
Similarity search - Domain/homology
Biological speciesThaumatococcus daniellii (katemfe)
Methodelectron crystallography / cryo EM / Resolution: 2.5 Å
Authorsde la Cruz MJ / Hattne J
CitationJournal: Nat Methods / Year: 2017
Title: Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.
Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P ...Authors: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P Hinck / Guillermo Calero / David Eisenberg / Tamir Gonen /
Abstract: Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from ...Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.
History
DepositionMay 26, 2016-
Header (metadata) releaseJun 22, 2016-
Map releaseJun 22, 2016-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5k7q
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5k7q
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8219.png

Downloads & links

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Map

FileDownload / File: emd_8219.map.gz / Format: CCP4 / Size: 1.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThaumatin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.85 Å/pix.
x 67 pix.
= 150.307 Å		0.81 Å/pix.
x 73 pix.
= 58.118 Å		0.81 Å/pix.
x 67 pix.
= 58.118 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.8072 Å / Y: 0.8072 Å / Z: 0.85402 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.022 / Movie #1: 0.018
Minimum - Maximum-0.047730263 - 0.0734553
Average (Standard dev.)-0.000023899915 (±0.0124288965)
SymmetrySpace group: 92
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-44-16-35
Dimensions736767
Spacing7272176
CellA: 58.1185 Å / B: 58.1185 Å / C: 150.30699 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.807194444444440.807194444444440.85401704545455
M x/y/z7272176
origin x/y/z0.0000.0000.000
length x/y/z58.11858.118150.307
α/β/γ90.00090.00090.000
start NX/NY/NZ-44-16-35
NX/NY/NZ736767
MAP C/R/S213
start NC/NR/NS-16-44-35
NC/NR/NS677367
D min/max/mean-0.0480.073-0.000

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Supplemental data

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Sample components

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Entire : Thaumatin

EntireName: Thaumatin
Components
  • Organelle or cellular component: Thaumatin
    • Protein or peptide: Thaumatin-1
  • Ligand: water

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Supramolecule #1: Thaumatin

SupramoleculeName: Thaumatin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thaumatococcus daniellii (katemfe)
Molecular weightTheoretical: 22.166 KDa

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Macromolecule #1: Thaumatin-1

MacromoleculeName: Thaumatin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thaumatococcus daniellii (katemfe)
Molecular weightTheoretical: 22.227059 KDa
SequenceString: ATFEIVNRCS YTVWAAASKG DAALDAGGRQ LNSGESWTIN VEPGTNGGKI WARTDCYFDD SGSGICKTGD CGGLLRCKRF GRPPTTLAE FSLNQYGKDY IDISNIKGFN VPMNFSPTTR GCRGVRCAAD IVGQCPAKLK APGGGCNDAC TVFQTSEYCC T TGKCGPTE ...String:
ATFEIVNRCS YTVWAAASKG DAALDAGGRQ LNSGESWTIN VEPGTNGGKI WARTDCYFDD SGSGICKTGD CGGLLRCKRF GRPPTTLAE FSLNQYGKDY IDISNIKGFN VPMNFSPTTR GCRGVRCAAD IVGQCPAKLK APGGGCNDAC TVFQTSEYCC T TGKCGPTE YSRFFKRLCP DAFSYVLDKP TTVTCPGSSN YRVTFCPTA

UniProtKB: Thaumatin I

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 18 / 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
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

BufferpH: 7 / Component - Concentration: 1.1 M / Component - Name: ammonium tartate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 3 / Number real images: 471 / Number diffraction images: 471 / Average exposure time: 4.1 sec. / Average electron dose: 0.004 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 2000 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Molecular replacementSoftware - Name: MOLREP (ver. 11.4.05) / Software - details: Starting model PDB ID 4ek0
Symmetry determination software listSoftware - Name: POINTLESS (ver. 1.10.21)
Merging software listSoftware - Name: AIMLESS (ver. 0.5.25)
Crystallography statisticsNumber intensities measured: 51116 / Number structure factors: 12786 / Fourier space coverage: 81.5 / R sym: 0.434 / R merge: 0.434 / Overall phase error: 28.74 / Overall phase residual: 41.7 / Phase error rejection criteria: 0 / High resolution: 2.11 Å / Shell - Shell ID: 1 / Shell - High resolution: 2.5 Å / Shell - Low resolution: 2.86 Å / Shell - Number structure factors: 2825 / Shell - Phase residual: 52.4 / Shell - Fourier space coverage: 92.2 / Shell - Multiplicity: 3.9

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Atomic model buiding 1

Initial modelPDB ID:

4ek0


Chain - Chain ID: A / Chain - Residue range: 1-207 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: OTHER
Output model

PDB-5k7q:
MicroED structure of thaumatin at 2.5 A resolution

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