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- EMDB-2314: Electron crystallographic studies on IP39 of Euglena gracilis -

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Basic information

Entry
Database: EMDB / ID: EMD-2314
TitleElectron crystallographic studies on IP39 of Euglena gracilis
Map dataReconstruction from 2D crystals of IP39
Sample
  • Sample: Euglena IP39
  • Protein or peptide: Alpha-type IP39
Function / homologymembrane / Alpha-type IP39
Function and homology information
Biological speciesEuglena gracilis (euglena)
Methodelectron crystallography / cryo EM / Resolution: 7.0 Å
AuthorsSuzuki H / Ito Y / Yamazaki Y / Mineta K / Uji M / Abe K / Tani K / Fujiyoshi Y / Tsukita S
CitationJournal: Nat Commun / Year: 2013
Title: The four-transmembrane protein IP39 of Euglena forms strands by a trimeric unit repeat.
Authors: Hiroshi Suzuki / Yasuyuki Ito / Yuji Yamazaki / Katsuhiko Mineta / Masami Uji / Kazuhiro Abe / Kazutoshi Tani / Yoshinori Fujiyoshi / Sachiko Tsukita /
Abstract: Euglenoid flagellates have striped surface structures comprising pellicles, which allow the cell shape to vary from rigid to flexible during the characteristic movement of the flagellates. In Euglena ...Euglenoid flagellates have striped surface structures comprising pellicles, which allow the cell shape to vary from rigid to flexible during the characteristic movement of the flagellates. In Euglena gracilis, the pellicular strip membranes are covered with paracrystalline arrays of a major integral membrane protein, IP39, a putative four-membrane-spanning protein with the conserved sequence motif of the PMP-22/EMP/MP20/Claudin superfamily. Here we report the three-dimensional structure of Euglena IP39 determined by electron crystallography. Two-dimensional crystals of IP39 appear to form a striated pattern of antiparallel double-rows in which trimeric IP39 units are longitudinally polymerised, resulting in continuously extending zigzag-shaped lines. Structural analysis revealed an asymmetric molecular arrangement in the trimer, and suggested that at least four different interactions between neighbouring protomers are involved. A combination of such multiple interactions would be important for linear strand formation of membrane proteins in a lipid bilayer.
History
DepositionFeb 12, 2013-
Header (metadata) releaseFeb 20, 2013-
Map releaseApr 24, 2013-
UpdateMay 8, 2013-
Current statusMay 8, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.25
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2314.png

Downloads & links

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Map

FileDownload / File: emd_2314.map.gz / Format: CCP4 / Size: 1.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction from 2D crystals of IP39
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.67 Å/pix.
x 121 pix.
= 200. Å		1.74 Å/pix.
x 101 pix.
= 174.3 Å		1.65 Å/pix.
x 37 pix.
= 59.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 1.743 Å / Y: 1.64722 Å / Z: 1.66667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.25 / Movie #1: 1.25
Minimum - Maximum-4.28529978 - 5.46199989
Average (Standard dev.)-0.0019457 (±0.99446481)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-50-18-60
Dimensions10137121
Spacing36100120
CellA: 174.3 Å / B: 59.3 Å / C: 200.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7431.64722222222221.6666666666667
M x/y/z10036120
origin x/y/z0.0000.0000.000
length x/y/z174.30059.300200.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-50-18-60
NX/NY/NZ10137121
MAP C/R/S213
start NC/NR/NS-18-50-60
NC/NR/NS37101121
D min/max/mean-4.2855.462-0.002

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Supplemental data

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Sample components

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Entire : Euglena IP39

EntireName: Euglena IP39
Components
  • Sample: Euglena IP39
  • Protein or peptide: Alpha-type IP39

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Supramolecule #1000: Euglena IP39

SupramoleculeName: Euglena IP39 / type: sample / ID: 1000 / Details: 2D array / Oligomeric state: Trimer / Number unique components: 12
Molecular weightTheoretical: 39 KDa

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Macromolecule #1: Alpha-type IP39

MacromoleculeName: Alpha-type IP39 / type: protein_or_peptide / ID: 1 / Name.synonym: Major integral plasma membrane protein / Number of copies: 12 / Oligomeric state: trimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Euglena gracilis (euglena) / Location in cell: Plasma membrane
Molecular weightTheoretical: 39 KDa
SequenceUniProtKB: Alpha-type IP39

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

Concentration0.35 mg/mL
BufferpH: 7
Details: 10 mM Hepes (pH7.0), 150 mM NaCl, 1 mM MgCl2, 30% (v/v) glycerol
GridDetails: carbon sandwich method
VitrificationCryogen name: NITROGEN / Instrument: LEICA KF80 / Details: Vitrification carried out at 4 degree.
DetailsCrystal growth by dialysis
Crystal formationDetails: Crystal growth by dialysis

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Electron microscopy

MicroscopeJEOL KYOTO-3000SFF
DateJul 13, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 310 / Bits/pixel: 8
Tilt angle min0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 3.32 µm / Nominal defocus min: 0.87 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Helium cooled / Specimen holder model: JEOL / Tilt angle max: 60 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 60 °

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Image processing

DetailsMRC package suite
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: OTHER / Software - Name: MRC
Crystal parametersUnit cell - A: 174.3 Å / Unit cell - B: 59.3 Å / Unit cell - C: 200.0 Å / Unit cell - γ: 90.0 ° / Unit cell - α: 90.0 ° / Unit cell - β: 90.0 ° / Plane group: P 2
CTF correctionDetails: Each micrographs

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