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- EMDB-8794: katanin hexamer in spiral conformation -

Open data

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Basic information

Database: EMDB / ID: 8794
Titlekatanin hexamer in spiral conformation
SourceCaenorhabditis elegans / animal /
Map data
Methodsingle particle reconstruction, at 4.4 Å resolution
AuthorsZehr EA / Szyk A / Piszczek G / Szczesna E / Zuo X / Roll-Mecak A
CitationNat. Struct. Mol. Biol., 2017, 24, 717-725

Nat. Struct. Mol. Biol., 2017, 24, 717-725 Yorodumi Papers
Katanin spiral and ring structures shed light on power stroke for microtubule severing.
Elena Zehr / Agnieszka Szyk / Grzegorz Piszczek / Ewa Szczesna / Xiaobing Zuo / Antonina Roll-Mecak

Validation ReportPDB-ID: 5wc0

SummaryFull reportAbout validation report
DateDeposition: Jun 29, 2017 / Header (metadata) release: Jul 12, 2017 / Map release: Aug 9, 2017 / Last update: Sep 20, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.043
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.043
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5wc0
  • Surface level: 0.043
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_8794.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.31 Å/pix.
= 393. Å
300 pix
1.31 Å/pix.
= 393. Å
300 pix
1.31 Å/pix.
= 393. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.31 Å
Contour Level:0.043 (by author), 0.043 (movie #1):
Minimum - Maximum-0.071658485 - 0.1452444
Average (Standard dev.)0.00019879645 (0.0032129025)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 392.99997 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z393.000393.000393.000
start NX/NY/NZ-34-26-36
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0720.1450.000

Supplemental data

Sample components

Entire katanin

EntireName: katanin / Number of components: 3
MassTheoretical: 310 kDa

Component #1: protein, katanin

ProteinName: katanin / Recombinant expression: No
MassTheoretical: 310 kDa
SourceSpecies: Caenorhabditis elegans / animal /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

Component #2: protein, Meiotic spindle formation protein mei-1

ProteinName: Meiotic spindle formation protein mei-1 / Recombinant expression: No
MassTheoretical: 51.802359 kDa
Source (engineered)Expression System: Caenorhabditis elegans / animal /

Component #3: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.6 mg/ml / pH: 7.5
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 90 %

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 51 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm
CameraDetector: GATAN K2 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 2100

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 38072
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

Atomic model buiding

Output model

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