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- EMDB-20762: Katanin hexamer in the ring conformation in complex with substrate -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-20762
TitleKatanin hexamer in the ring conformation in complex with substrate
Map data
SampleHexameric complex of C.elegans katanin bound to polyglutamate peptide:
Meiotic spindle formation protein mei-1 / Polyglutamate peptide / (ligand) x 2
Function / homology
Function and homology information


negative regulation of meiotic spindle elongation / MATH domain binding / katanin complex / meiotic spindle disassembly / microtubule severing / microtubule-severing ATPase / microtubule-severing ATPase activity / female meiotic nuclear division / meiotic spindle organization / striated muscle myosin thick filament assembly ...negative regulation of meiotic spindle elongation / MATH domain binding / katanin complex / meiotic spindle disassembly / microtubule severing / microtubule-severing ATPase / microtubule-severing ATPase activity / female meiotic nuclear division / meiotic spindle organization / striated muscle myosin thick filament assembly / embryo development ending in birth or egg hatching / microtubule depolymerization / protein hexamerization / cytoplasmic microtubule organization / isomerase activity / spindle / spindle pole / chromosome / microtubule / microtubule binding / protein phosphatase binding / ATPase activity / centrosome / cell division / ATP binding / identical protein binding / nucleus
ATPase, AAA-type, core / AAA+ ATPase domain / AAA-protein family signature. / AAA+ lid domain / ATPase family associated with various cellular activities (AAA) / AAA ATPase, AAA+ lid domain / Katanin p60 subunit A1 / P-loop containing nucleoside triphosphate hydrolase / ATPase, AAA-type, conserved site
Meiotic spindle formation protein mei-1
Biological speciesCaenorhabditis elegans (roundworm) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZehr EA / Roll-Mecak A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke1 ZIA NS003165 United States
CitationJournal: To Be Published
Title: Katanin grips the b-tubulin tail through an electropositive double spiral to sever microtubules
Authors: Zehr EA / Szyk A / Szczesna E / Roll-Mecak A
Validation ReportPDB-ID: 6uge

SummaryFull reportAbout validation report
History
DepositionSep 26, 2019-
Header (metadata) releaseOct 9, 2019-
Map releaseOct 9, 2019-
UpdateOct 9, 2019-
Current statusOct 9, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.74
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.74
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6uge
  • Surface level: 5.74
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20762.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 224 pix.
= 241.92 Å
1.08 Å/pix.
x 224 pix.
= 241.92 Å
1.08 Å/pix.
x 224 pix.
= 241.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 5.74 / Movie #1: 5.74
Minimum - Maximum-17.770409999999998 - 30.53059
Average (Standard dev.)0.000000000000396 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 241.92001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z241.920241.920241.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ224224224
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-17.77030.5310.000

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Supplemental data

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Sample components

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Entire Hexameric complex of C.elegans katanin bound to polyglutamate peptide

EntireName: Hexameric complex of C.elegans katanin bound to polyglutamate peptide
Number of components: 5

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Component #1: protein, Hexameric complex of C.elegans katanin bound to polyglut...

ProteinName: Hexameric complex of C.elegans katanin bound to polyglutamate peptide
Recombinant expression: No
MassTheoretical: 312 kDa
SourceSpecies: Caenorhabditis elegans (roundworm)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pDEST566 / Strain: BL21(DE3)

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

ProteinName: Meiotic spindle formation protein mei-1 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 53.576336 kDa
SourceSpecies: Caenorhabditis elegans (roundworm)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: protein, Polyglutamate peptide

ProteinName: Polyglutamate peptide / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.567381 kDa
SourceSpecies: synthetic construct (others)

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Component #4: ligand, ADENOSINE-5'-TRIPHOSPHATE

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

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Component #5: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / pH: 7.5
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 279.15 K / Humidity: 90 % / Details: Load 5 ul sample, wait 10 sec, blot 4.5 sec.

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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: 73 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2800.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (93.0 - 103.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5911

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 108700
Details: Frames were aligned, dose weighted and summed using MotionCor2
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Correlation coefficient / Refinement space: REAL
Input PDB model: 5WC0
Output model

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