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- EMDB-4172: Roadblock-1 region of the dynein tail/dynactin/BICDR1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4172
TitleRoadblock-1 region of the dynein tail/dynactin/BICDR1 complex
Map data
Sample
  • Complex: Two dynein tail domains, dynactin and BICDR1
    • Protein or peptide: Cytoplasmic dynein 1 intermediate chain 2
    • Protein or peptide: Dynein light chain roadblock-type 1
Function / homology
Function and homology information


transport along microtubule / visual behavior / dynein light chain binding / dynein heavy chain binding / ciliary tip / Intraflagellar transport / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / microtubule motor activity ...transport along microtubule / visual behavior / dynein light chain binding / dynein heavy chain binding / ciliary tip / Intraflagellar transport / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / microtubule motor activity / dynein intermediate chain binding / microtubule-based movement / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / MHC class II antigen presentation / AURKA Activation by TPX2 / RHO GTPases Activate Formins / cilium / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / vesicle / microtubule / centrosome / membrane / cytosol / cytoplasm
Similarity search - Function
Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein light chain roadblock-type 1/2 / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats circular profile. ...Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein light chain roadblock-type 1/2 / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Cytoplasmic dynein 1 intermediate chain 2 / Dynein light chain roadblock-type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsUrnavicius L / Lau CK / Elshenawy MM / Morales-Rios E / Motz C / Yildiz A / Carter AP
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_A025_1011 United Kingdom
Wellcome TrustWT100387 United Kingdom
CitationJournal: Nature / Year: 2018
Title: Cryo-EM shows how dynactin recruits two dyneins for faster movement.
Authors: Linas Urnavicius / Clinton K Lau / Mohamed M Elshenawy / Edgar Morales-Rios / Carina Motz / Ahmet Yildiz / Andrew P Carter /
Abstract: Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. ...Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. Here we use electron microscopy and single-molecule studies to show that adaptors can recruit a second dynein to dynactin. Whereas BICD2 is biased towards recruiting a single dynein, the adaptors BICDR1 and HOOK3 predominantly recruit two dyneins. We find that the shift towards a double dynein complex increases both the force and speed of the microtubule motor. Our 3.5 Å resolution cryo-electron microscopy reconstruction of a dynein tail-dynactin-BICDR1 complex reveals how dynactin can act as a scaffold to coordinate two dyneins side-by-side. Our work provides a structural basis for understanding how diverse adaptors recruit different numbers of dyneins and regulate the motile properties of the dynein-dynactin transport machine.
History
DepositionNov 23, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseJan 17, 2018-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.131
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.131
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6f1z
  • Surface level: 0.131
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6f1z
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4172.png

Downloads & links

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Map

FileDownload / File: emd_4172.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.131 / Movie #1: 0.131
Minimum - Maximum-0.23592894 - 0.3543181
Average (Standard dev.)-0.00018600347 (±0.004345116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 804.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z804.000804.000804.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.2360.354-0.000

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Supplemental data

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Sample components

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Entire : Two dynein tail domains, dynactin and BICDR1

EntireName: Two dynein tail domains, dynactin and BICDR1
Components
  • Complex: Two dynein tail domains, dynactin and BICDR1
    • Protein or peptide: Cytoplasmic dynein 1 intermediate chain 2
    • Protein or peptide: Dynein light chain roadblock-type 1

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Supramolecule #1: Two dynein tail domains, dynactin and BICDR1

SupramoleculeName: Two dynein tail domains, dynactin and BICDR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Cytoplasmic dynein 1 intermediate chain 2

MacromoleculeName: Cytoplasmic dynein 1 intermediate chain 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.442141 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSDKSELKAE LERKKQRLAQ IREEKKRKEE ERKKKETDQK KEAVAPVQEE SDLEKKRREA EALLQSMGLT PESPIVPPPM SPSSKSVST PSEAGSQDSG DGAVGSRRGP IKLGMAKITQ VDFPPREIVT YTKETQTPVM AQPKEDEEED DDVVAPKPPI E PEEEKTLK ...String:
MSDKSELKAE LERKKQRLAQ IREEKKRKEE ERKKKETDQK KEAVAPVQEE SDLEKKRREA EALLQSMGLT PESPIVPPPM SPSSKSVST PSEAGSQDSG DGAVGSRRGP IKLGMAKITQ VDFPPREIVT YTKETQTPVM AQPKEDEEED DDVVAPKPPI E PEEEKTLK KDEENDSKAP PHELTEEEKQ QILHSEEFLS FFDHSTRIVE RALSEQINIF FDYSGRDLED KEGEIQAGAK LS LNRQFFD ERWSKHRVVS CLDWSSQYPE LLVASYNNNE DAPHEPDGVA LVWNMKYKKT TPEYVFHCQS AVMSATFAKF HPN LVVGGT YSGQIVLWDN RSNKRTPVQR TPLSAAAHTH PVYCVNVVGT QNAHNLISIS TDGKICSWSL DMLSHPQDSM ELVH KQSKA VAVTSMSFPV GDVNNFVVGS EEGSVYTACR HGSKAGISEM FEGHQGPITG IHCHAAVGAV DFSHLFVTSS FDWTV KLWS TKNNKPLYSF EDNAGYVYDV MWSPTHPALF ACVDGMGRLD LWNLNNDTEV PTASISVEGN PALNRVRWTH SGREIA VGD SEGQIVIYDV GEQIAVPRND EWARFGRTLA EINANRADAE EEAATRIPA

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Macromolecule #2: Dynein light chain roadblock-type 1

MacromoleculeName: Dynein light chain roadblock-type 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.934576 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAEVEETLKR LQSQKGVQGI IVVNTEGIPI KSTMDNPTTT QYASLMHSFI LKARSTVRDI DPQNDLTFLR IRSKKNEIMV APDKDYFLI VIQNPTE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: EMDB MAP
EMDB ID:

2860


Details: Initial model low pass filtered to 50 A
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Details: Masked 3D classification on Roadblock-1, no alignments
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Details: Signal for dynactin and N-terminal regions of dynein heavy chain subtracted from raw particles.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 77136

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-6f1z:
Roadblock-1 region of the dynein tail/dynactin/BICDR1 complex

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