[English] 日本語
Yorodumi
- EMDB-6016: Dynein motor domain in complex with Lis1 in the presence of ATP and Vi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6016
TitleDynein motor domain in complex with Lis1 in the presence of ATP and Vi
Map dataReconstruction of dynein motor domain in complex with Lis1 in the presence of ATP and Vi
Sample
  • Sample: Dynein motor domain in complex with Lis1 in 500 uM ATP/NaVO4
  • Protein or peptide: Dynein heavy chain
  • Protein or peptide: Lis1
Keywordsdynein / lis1 / regulation mechanism
Function / homology
Function and homology information


microtubule sliding / karyogamy / microtubule organizing center organization / nuclear migration along microtubule / astral microtubule / establishment of mitotic spindle localization / microtubule plus-end binding / spindle pole body / vesicle transport along microtubule / minus-end-directed microtubule motor activity ...microtubule sliding / karyogamy / microtubule organizing center organization / nuclear migration along microtubule / astral microtubule / establishment of mitotic spindle localization / microtubule plus-end binding / spindle pole body / vesicle transport along microtubule / minus-end-directed microtubule motor activity / microtubule associated complex / cytoplasmic dynein complex / dynein light intermediate chain binding / nuclear migration / dynein intermediate chain binding / dynein complex binding / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / Antigen processing: Ubiquitination & Proteasome degradation / cytoplasmic microtubule / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / kinetochore / spindle pole / nuclear envelope / cell cortex / cell division / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Dynein regulator LIS1 / LIS1, N-terminal / : / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, ATPase lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / Dynein heavy chain region D6 P-loop domain ...Dynein regulator LIS1 / LIS1, N-terminal / : / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, ATPase lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynein heavy chain, cytoplasmic / Nuclear distribution protein PAC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 23.1 Å
AuthorsToropova K / Zou S / Roberts AJ / Redwine WB / Goodman BS / Reck-Peterson SL / Leschziner AE
CitationJournal: Elife / Year: 2014
Title: Lis1 regulates dynein by sterically blocking its mechanochemical cycle.
Authors: Katerina Toropova / Sirui Zou / Anthony J Roberts / William B Redwine / Brian S Goodman / Samara L Reck-Peterson / Andres E Leschziner /
Abstract: Regulation of cytoplasmic dynein's motor activity is essential for diverse eukaryotic functions, including cell division, intracellular transport, and brain development. The dynein regulator Lis1 is ...Regulation of cytoplasmic dynein's motor activity is essential for diverse eukaryotic functions, including cell division, intracellular transport, and brain development. The dynein regulator Lis1 is known to keep dynein bound to microtubules; however, how this is accomplished mechanistically remains unknown. We have used three-dimensional electron microscopy, single-molecule imaging, biochemistry, and in vivo assays to help establish this mechanism. The three-dimensional structure of the dynein-Lis1 complex shows that binding of Lis1 to dynein's AAA+ ring sterically prevents dynein's main mechanical element, the 'linker', from completing its normal conformational cycle. Single-molecule experiments show that eliminating this block by shortening the linker to a point where it can physically bypass Lis1 renders single dynein motors insensitive to regulation by Lis1. Our data reveal that Lis1 keeps dynein in a persistent microtubule-bound state by directly blocking the progression of its mechanochemical cycle.
History
DepositionAug 3, 2014-
Header (metadata) releaseSep 24, 2014-
Map releaseNov 19, 2014-
UpdateNov 19, 2014-
Current statusNov 19, 2014Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6016.gif

Downloads & links

-
Map

FileDownload / File: emd_6016.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of dynein motor domain in complex with Lis1 in the presence of ATP and Vi
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.73 Å/pix.
x 180 pix.
= 311.4 Å		1.73 Å/pix.
x 180 pix.
= 311.4 Å		1.73 Å/pix.
x 180 pix.
= 311.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-6.25472641 - 10.28431892
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-90
Dimensions180180180
Spacing180180180
CellA=B=C: 311.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.731.731.73
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z311.400311.400311.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-90-90-90
NC/NR/NS180180180
D min/max/mean-6.25510.2840.000

-
Supplemental data

-
Supplemental map: emd 6016 half map 1.map

Fileemd_6016_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Supplemental map: emd 6016 half map 2.map

Fileemd_6016_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Dynein motor domain in complex with Lis1 in 500 uM ATP/NaVO4

EntireName: Dynein motor domain in complex with Lis1 in 500 uM ATP/NaVO4
Components
  • Sample: Dynein motor domain in complex with Lis1 in 500 uM ATP/NaVO4
  • Protein or peptide: Dynein heavy chain
  • Protein or peptide: Lis1

-
Supramolecule #1000: Dynein motor domain in complex with Lis1 in 500 uM ATP/NaVO4

SupramoleculeName: Dynein motor domain in complex with Lis1 in 500 uM ATP/NaVO4
type: sample / ID: 1000
Oligomeric state: One motor domain to one Lis1 propeller domain
Number unique components: 2
Molecular weightExperimental: 445 KDa / Theoretical: 445 KDa

-
Macromolecule #1: Dynein heavy chain

MacromoleculeName: Dynein heavy chain / type: protein_or_peptide / ID: 1 / Name.synonym: DYN1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: RPY1302 / synonym: Yeast / Location in cell: Cytoplasmic
Molecular weightExperimental: 331 KDa / Theoretical: 331 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: RPY1302
SequenceUniProtKB: Dynein heavy chain, cytoplasmic

-
Macromolecule #2: Lis1

MacromoleculeName: Lis1 / type: protein_or_peptide / ID: 2 / Name.synonym: Pac1 / Details: Only a single copy of Lis1 is resolved in the map. / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: RPY816 / synonym: Yeast / Location in cell: Cytoplasmic
Molecular weightExperimental: 57 KDa / Theoretical: 57 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: RPY816
SequenceUniProtKB: Nuclear distribution protein PAC1

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.03 mg/mL
BufferpH: 8
Details: 50 mM Tris-HCl, 150 mM potassium acetate, 2 mM magnesium acetate, 1 mM EGTA, 1 mM DTT, 500 uM Mg-ATP/NaVO4
StainingType: NEGATIVE
Details: Grids with adsorbed protein were floated on 2% w/v uranyl formate, then sandwiched with a thin layer of carbon, blotted, and frozen in liquid nitrogen.
GridDetails: 200 mesh C-flat grid with thin carbon support
VitrificationCryogen name: NITROGEN / Instrument: OTHER
Method: Manually blot, wait 10-20 seconds, then manually plunge into liquid nitrogen.

-
Electron microscopy

MicroscopeFEI TECNAI 20
DateMar 19, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 103 / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 86800 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.51 µm / Nominal magnification: 62000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

-
Image processing

CTF correctionDetails: phase flip
Final reconstructionResolution.type: BY AUTHOR / Resolution: 23.1 Å / Resolution method: OTHER / Software - Name: RELION
Details: The dataset was first 3D-classified in RELION. Particles in this map displayed a resolved linker domain at lower contour levels.
Number images used: 1072

-
Atomic model buiding 1

Initial modelPDB ID:

4akg


Chain - Chain ID: A
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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