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- EMDB-4117: cryoEM structure of crenactin double helical filament at 3.8A res... -

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Basic information

Entry
Database: EMDB / ID: EMD-4117
TitlecryoEM structure of crenactin double helical filament at 3.8A resolution
Map data
Sample
  • Complex: crenactin
    • Protein or peptide: Actin/actin family protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoskeleton / hydrolase activity / ATP binding / cytoplasm
Similarity search - Function
Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Biological speciesPyrobaculum calidifontis (archaea) / Pyrobaculum calidifontis (strain JCM 11548 / VA1) (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsIzore T / Lowe J
CitationJournal: Elife / Year: 2016
Title: Crenactin forms actin-like double helical filaments regulated by arcadin-2.
Authors: Thierry Izoré / Danguole Kureisaite-Ciziene / Stephen H McLaughlin / Jan Löwe /
Abstract: The similarity of eukaryotic actin to crenactin, a filament-forming protein from the crenarchaeon supports the theory of a common origin of Crenarchaea and Eukaryotes. Monomeric structures of ...The similarity of eukaryotic actin to crenactin, a filament-forming protein from the crenarchaeon supports the theory of a common origin of Crenarchaea and Eukaryotes. Monomeric structures of crenactin and actin are similar, although their filament architectures were suggested to be different. Here we report that crenactin forms double helical filaments that show exceptional similarity to eukaryotic F-actin. With cryo-electron microscopy and helical reconstruction we solved the structure of the crenactin filament to 3.8 Å resolution. When forming double filaments, the 'hydrophobic plug' loop in crenactin rearranges. Arcadin-2, also encoded by the arcade gene cluster, binds tightly with its C-terminus to the hydrophobic groove of crenactin. Binding is reminiscent of eukaryotic actin modulators such as cofilin and thymosin β4 and arcadin-2 is a depolymeriser of crenactin filaments. Our work further supports the theory of shared ancestry of Eukaryotes and Crenarchaea.
History
DepositionSep 23, 2016-
Header (metadata) releaseOct 26, 2016-
Map releaseJan 18, 2017-
UpdateJan 18, 2017-
Current statusJan 18, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.128
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.128
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5mw1
  • Surface level: 0.128
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5mw1
  • Surface level: 0.128
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5mw1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4117.png

Downloads & links

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Map

FileDownload / File: emd_4117.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 280 pix.
= 375.2 Å		1.34 Å/pix.
x 280 pix.
= 375.2 Å		1.34 Å/pix.
x 280 pix.
= 375.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.128 / Movie #1: 0.128
Minimum - Maximum-0.39248633 - 0.7795027
Average (Standard dev.)-0.00007327642 (±0.024862617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 375.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z375.200375.200375.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.3920.780-0.000

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Supplemental data

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Sample components

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Entire : crenactin

EntireName: crenactin
Components
  • Complex: crenactin
    • Protein or peptide: Actin/actin family protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: crenactin

SupramoleculeName: crenactin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrobaculum calidifontis (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pOPIN-S

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Macromolecule #1: Actin/actin family protein

MacromoleculeName: Actin/actin family protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pyrobaculum calidifontis (strain JCM 11548 / VA1) (archaea)
Strain: JCM 11548 / VA1
Molecular weightTheoretical: 48.425484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGVISDAYRL KYTFGVDFGT SYVKYGPITL NEPKMVQTRG LFLRDLPESV KMRIPPDVLA RGLVVGDEEV RKYLSSVRDV QRNLKYPLK DGVARRDDEE AWRVLKELAR YTLAQFPVSD PEFAGWLVAV ALSALAPDYM YKAIFDIYDE LASEFKIYAV T ILPQPLAV ...String:
MGVISDAYRL KYTFGVDFGT SYVKYGPITL NEPKMVQTRG LFLRDLPESV KMRIPPDVLA RGLVVGDEEV RKYLSSVRDV QRNLKYPLK DGVARRDDEE AWRVLKELAR YTLAQFPVSD PEFAGWLVAV ALSALAPDYM YKAIFDIYDE LASEFKIYAV T ILPQPLAV AIAENAVNCV IVEGGHGNIQ VAPISFALIR EGLVALNRGG AEANAITREI LKDIGYSDIA REEYAVEVVK RA VGLVPRR LKEAIRAAKS DPDRFVTKVR LSPVVEVEIP REYAWTRFLI GEIVFDPNHE EIKSYIEQSR LRIENAVIGD VTL YGEMDV ASAIITSLRN VSVEIQERVA SQIILSGGAF SWRVPPGMED VAADSVTRVK IALEEKSPAL ASKVEVRLVS EPQY SVWRG AVIYGYALPL SLEWSDTTRE GWRFPRR

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number real images: 1474 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsFalcon III prototype at 46 frames per second
Final reconstructionApplied symmetry - Helical parameters - Δz: 25.6 Å
Applied symmetry - Helical parameters - Δ&Phi: -161.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0)
Details: Helical segments divided at the filament level into the two half sets at the beginning.
Number images used: 470396
CTF correctionSoftware - Name: GCTF
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4cj7

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER / Target criteria: R-factor & stereochemistry
Output model

PDB-5mw1:
cryoEM structure of crenactin double helical filament at 3.8A resolution

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