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- EMDB-7056: Dimer of stromal portion of ARC6 -

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Basic information

Entry
Database: EMDB / ID: EMD-7056
TitleDimer of stromal portion of ARC6
Map dataStromal portion of ARC6
Sample
  • Organelle or cellular component: ARC6
    • Other: ARC6
KeywordsARC6 / plastid / chloroplast / FtsZ / STRUCTURAL PROTEIN
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / negative staining / Resolution: 22.0 Å
AuthorsSung MW
CitationJournal: J Biol Chem / Year: 2018
Title: The chloroplast division protein ARC6 acts to inhibit disassembly of GDP-bound FtsZ2.
Authors: Min Woo Sung / Rahamthulla Shaik / Allan D TerBush / Katherine W Osteryoung / Stanislav Vitha / Andreas Holzenburg /
Abstract: Chloroplasts host photosynthesis and fulfill other metabolic functions that are essential to plant life. They have to divide by binary fission to maintain their numbers throughout cycles of cell ...Chloroplasts host photosynthesis and fulfill other metabolic functions that are essential to plant life. They have to divide by binary fission to maintain their numbers throughout cycles of cell division. Chloroplast division is achieved by a complex ring-shaped division machinery located on both the inner (stromal) and the outer (cytosolic) side of the chloroplast envelope. The inner division ring (termed the Z ring) is formed by the assembly of tubulin-like FtsZ1 and FtsZ2 proteins. ARC6 is a key chloroplast division protein that interacts with the Z ring. ARC6 spans the inner envelope membrane, is known to stabilize or maintain the Z ring, and anchors the Z ring to the inner membrane through interaction with FtsZ2. The underlying mechanism of Z ring stabilization is not well-understood. Here, biochemical and structural characterization of ARC6 was conducted using light scattering, sedimentation, and light and transmission EM. The recombinant protein was purified as a dimer. The results indicated that a truncated form of ARC6 (tARC6), representing the stromal portion of ARC6, affects FtsZ2 assembly without forming higher-order structures and exerts its effect via FtsZ2 dynamics. tARC6 prevented GDP-induced FtsZ2 disassembly and caused a significant net increase in FtsZ2 assembly when GDP was present. Single particle analysis and 3D reconstruction were performed to elucidate the structural basis of ARC6 activity. Together, the data reveal that a dimeric form of tARC6 binds to FtsZ2 filaments and does not increase FtsZ polymerization rates but rather inhibits GDP-associated FtsZ2 disassembly.
History
DepositionSep 29, 2017-
Header (metadata) releaseNov 8, 2017-
Map releaseOct 3, 2018-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.9
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7056.png

Downloads & links

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Map

FileDownload / File: emd_7056.map.gz / Format: CCP4 / Size: 251 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStromal portion of ARC6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.1 Å/pix.
x 40 pix.
= 204. Å		5.1 Å/pix.
x 40 pix.
= 204. Å		5.1 Å/pix.
x 40 pix.
= 204. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.9 / Movie #1: 3.9
Minimum - Maximum-5.1198225 - 7.9471645
Average (Standard dev.)-0.000000000015953 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-20-20-20
Dimensions404040
Spacing404040
CellA=B=C: 204.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.15.15.1
M x/y/z404040
origin x/y/z0.0000.0000.000
length x/y/z204.000204.000204.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ416416416
MAP C/R/S123
start NC/NR/NS-20-20-20
NC/NR/NS404040
D min/max/mean-5.1207.947-0.000

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Supplemental data

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Sample components

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Entire : ARC6

EntireName: ARC6
Components
  • Organelle or cellular component: ARC6
    • Other: ARC6

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Supramolecule #1: ARC6

SupramoleculeName: ARC6 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 106.9 KDa

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Macromolecule #1: ARC6

MacromoleculeName: ARC6 / type: other / ID: 1 / Classification: other
SequenceString: DFYQVLGAQT HFLTDGIRRA FEARVSKPPQ FGFSDDALIS RRQILQAACE TLSNPRSRRE YNEGLLDDEE ATVITDVPWD KVPGALCVLQ EGGETEIVLR VGEALLKERL PKSFKQDVVL VMALAFLDVS RDAMALDPPD FITGYEFVEE ALKLLQEEGA SSLAPDLRAQ ...String:
DFYQVLGAQT HFLTDGIRRA FEARVSKPPQ FGFSDDALIS RRQILQAACE TLSNPRSRRE YNEGLLDDEE ATVITDVPWD KVPGALCVLQ EGGETEIVLR VGEALLKERL PKSFKQDVVL VMALAFLDVS RDAMALDPPD FITGYEFVEE ALKLLQEEGA SSLAPDLRAQ IDETLEEITP RYVLELLGLP LGDDYAAKRL NGLSGVRNIL WSVGGGGASA LVGGLTREKF MNEAFLRMTA AEQVDLFVAT PSNIPAESFE VYEVALALVA QAFIGKKPHL LQDADKQFQQ LQQAKVMAME IPAMLYDTRN NWEIDFGLER GLCALLIGKV DECRMWLGLD SEDSQYRNPA IVEFVLENSN RDDNDDLPGL CKLLETWLAG VVFPRFRDTK DKKFKLGDYY DDPMVLSYLE RVEVVQGSPL AAAAAMARIG A

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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

Concentration0.07 mg/mL
BufferpH: 7.5
StainingType: NEGATIVE / Material: 2% Uranyl Acetate
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS

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Electron microscopy

MicroscopeJEOL 1200EX
Image recordingFilm or detector model: SIA 15C (3k x 3k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER

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Image processing

Startup modelType of model: OTHER / Details: reference free class averages
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN (ver. 1) / Number images used: 4121
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: OTHER

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