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- EMDB-3717: Structure of differently sized plant protein -

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Basic information

Entry
Database: EMDB / ID: EMD-3717
TitleStructure of differently sized plant protein
Map dataIM30 in C15 symmetrical ring assembly
Sample
  • Complex: Structure of a C15-symmetrical IM30 ring assembly
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsSaur M / Hennig R / Young P / Rusitzka K / Hellmann N / Heidrich J / Morgner N / Markl J / Schneider D
CitationJournal: Structure / Year: 2017
Title: A Janus-Faced IM30 Ring Involved in Thylakoid Membrane Fusion Is Assembled from IM30 Tetramers.
Authors: Michael Saur / Raoul Hennig / Phoebe Young / Kristiane Rusitzka / Nadja Hellmann / Jennifer Heidrich / Nina Morgner / Jürgen Markl / Dirk Schneider /
Abstract: Biogenesis and dynamics of thylakoid membranes likely involves membrane fusion events. Membrane attachment of the inner membrane-associated protein of 30 kDa (IM30) affects the structure of the ...Biogenesis and dynamics of thylakoid membranes likely involves membrane fusion events. Membrane attachment of the inner membrane-associated protein of 30 kDa (IM30) affects the structure of the lipid bilayer, finally resulting in membrane fusion. Yet, how IM30 triggers membrane fusion is largely unclear. IM30 monomers pre-assemble into stable tetrameric building blocks, which further align to form oligomeric ring structures, and differently sized IM30 rings bind to membranes. Based on a 3D reconstruction of IM30 rings, we locate the IM30 loop 2 region at the bottom of the ring and show intact membrane binding but missing fusogenic activity of loop 2 mutants. However, helix 7, which has recently been shown to mediate membrane binding, was located at the oppossite, top side of IM30 rings. We propose that a two-sided IM30 ring complex connects two opposing membranes, finally resulting in membrane fusion. Thus, IM30-mediated membrane fusion requires a Janus-faced IM30 ring.
History
DepositionMay 10, 2017-
Header (metadata) releaseJun 14, 2017-
Map releaseAug 23, 2017-
UpdateNov 4, 2020-
Current statusNov 4, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.89
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.89
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3717.png

Downloads & links

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Map

FileDownload / File: emd_3717.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIM30 in C15 symmetrical ring assembly
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.36 Å/pix.
x 128 pix.
= 558.08 Å		4.36 Å/pix.
x 128 pix.
= 558.08 Å		4.36 Å/pix.
x 128 pix.
= 558.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.89 / Movie #1: 0.89
Minimum - Maximum-0.84859186 - 2.577232
Average (Standard dev.)0.04878561 (±0.25888634)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-63-63-63
Dimensions128128128
Spacing128128128
CellA=B=C: 558.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.364.364.36
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z558.080558.080558.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-63-63-63
NC/NR/NS128128128
D min/max/mean-0.8492.5770.049

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Supplemental data

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Sample components

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Entire : Structure of a C15-symmetrical IM30 ring assembly

EntireName: Structure of a C15-symmetrical IM30 ring assembly
Components
  • Complex: Structure of a C15-symmetrical IM30 ring assembly

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Supramolecule #1: Structure of a C15-symmetrical IM30 ring assembly

SupramoleculeName: Structure of a C15-symmetrical IM30 ring assembly / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.8 MDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 4503
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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