[English] 日本語
Yorodumi
- EMDB-8794: katanin hexamer in spiral conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8794
Titlekatanin hexamer in spiral conformation
Map data
Sample
  • Complex: katanin
    • Protein or peptide: Meiotic spindle formation protein mei-1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsMicrotubule cytoskeleton / microtubule-severing enzyme / AAA ATPase / p60 / MOTOR PROTEIN
Function / homology
Function and homology information


negative regulation of meiotic spindle elongation / MATH domain binding / striated muscle myosin thick filament assembly / meiotic spindle disassembly / katanin complex / meiotic spindle pole / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / female meiotic nuclear division ...negative regulation of meiotic spindle elongation / MATH domain binding / striated muscle myosin thick filament assembly / meiotic spindle disassembly / katanin complex / meiotic spindle pole / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / female meiotic nuclear division / meiotic spindle organization / embryo development ending in birth or egg hatching / meiotic spindle / microtubule depolymerization / spindle / spindle pole / protein phosphatase binding / microtubule binding / molecular adaptor activity / microtubule / cell division / centrosome / chromatin / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Katanin p60 subunit A1 / : / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Meiotic spindle formation protein mei-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsZehr EA / Szyk A / Piszczek G / Szczesna E / Zuo X / Roll-Mecak A
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: Katanin spiral and ring structures shed light on power stroke for microtubule severing.
Authors: Elena Zehr / Agnieszka Szyk / Grzegorz Piszczek / Ewa Szczesna / Xiaobing Zuo / Antonina Roll-Mecak /
Abstract: Microtubule-severing enzymes katanin, spastin and fidgetin are AAA ATPases important for the biogenesis and maintenance of complex microtubule arrays in axons, spindles and cilia. Because of a lack ...Microtubule-severing enzymes katanin, spastin and fidgetin are AAA ATPases important for the biogenesis and maintenance of complex microtubule arrays in axons, spindles and cilia. Because of a lack of known 3D structures for these enzymes, their mechanism of action has remained poorly understood. Here we report the X-ray crystal structure of the monomeric AAA katanin module from Caenorhabditis elegans and cryo-EM reconstructions of the hexamer in two conformations. The structures reveal an unexpected asymmetric arrangement of the AAA domains mediated by structural elements unique to microtubule-severing enzymes and critical for their function. The reconstructions show that katanin cycles between open spiral and closed ring conformations, depending on the ATP occupancy of a gating protomer that tenses or relaxes interprotomer interfaces. Cycling of the hexamer between these conformations would provide the power stroke for microtubule severing.
History
DepositionJun 29, 2017-
Header (metadata) releaseJul 12, 2017-
Map releaseAug 9, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • 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
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8794.png

Downloads & links

-
Map

FileDownload / File: emd_8794.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 300 pix.
= 393. Å		1.31 Å/pix.
x 300 pix.
= 393. Å		1.31 Å/pix.
x 300 pix.
= 393. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.043 / Movie #1: 0.043
Minimum - Maximum-0.071658485 - 0.1452444
Average (Standard dev.)0.00019879645 (±0.0032129025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 392.99997 Å
α=β=γ: 90.0 °

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
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0720.1450.000

-
Supplemental data

-
Sample components

-
Entire : katanin

EntireName: katanin
Components
  • Complex: katanin
    • Protein or peptide: Meiotic spindle formation protein mei-1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: katanin

SupramoleculeName: katanin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 310 KDa

-
Macromolecule #1: Meiotic spindle formation protein mei-1

MacromoleculeName: Meiotic spindle formation protein mei-1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: ec: 3.6.4.3
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 51.802359 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNGDVQSVIR GYLERAQVAK TMSDAGRWNE AGDLLRQLMT DVKSCKISAS NRDEHDARNT FLRALEANLK LVQQNVRDED DLHEAMTRQ SGSPEPPADP DVWSKPSPPL PSSSKFGATK KGVGAAGPRP REISKSTSSM STNPADVKPA NPTQGILPQN S AGDSFDAS ...String:
MNGDVQSVIR GYLERAQVAK TMSDAGRWNE AGDLLRQLMT DVKSCKISAS NRDEHDARNT FLRALEANLK LVQQNVRDED DLHEAMTRQ SGSPEPPADP DVWSKPSPPL PSSSKFGATK KGVGAAGPRP REISKSTSSM STNPADVKPA NPTQGILPQN S AGDSFDAS AYDAYIVQAV RGTMATNTEN TMSLDDIIGM HDVKQVLHEA VTLPLLVPEF FQGLRSPWKA MVLAGPPGTG KT LIARAIA SESSSTFFTV SSTDLSSKWR GDSEKIVRLL FELARFYAPS IIFIDQIDTL GGQRGNSGEH EASRRVKSEF LVQ MDGSQN KFDSRRVFVL AATNIPWELD EALRRRFEKR IFIPLPDIDA RKKLIEKSME GTPKSDEINY DDLAARTEGF SGAD VVSLC RTAAINVLRR YDTKSLRGGE LTAAMESLKA ELVRNIDFEA ALQAVSPSAG PDTMLKCKEW CDSFGAM

UniProtKB: Meiotic spindle formation protein mei-1

-
Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.5
GridModel: C-flat / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 40 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 6 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA EM GP
DetailsAsembled in 1mM ATP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Number real images: 2100 / Average exposure time: 17.5 sec. / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 403023
Startup modelType of model: OTHER / Details: Generated de novo with FREALIGN
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 38072
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 3 / Avg.num./class: 50000 / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5wc0:
katanin hexamer in spiral conformation

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more