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- EMDB-4171: Dynein light intermediate chain region of the dynein tail/dynacti... -

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Basic information

Entry
Database: EMDB / ID: EMD-4171
TitleDynein light intermediate chain region of the dynein tail/dynactin/BICDR1 complex
Map dataMap of C terminal half of dynein tail in complex with dynactin and BICDR1, focussed on light intermediate chain.
Sample
  • Complex: Two dynein tail domains bound to dynactin and BICDR1
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain
    • Protein or peptide: Cytoplasmic dynein 1 light intermediate chain 2
KeywordsCryo-EM / Complex / MOTOR PROTEIN
Function / homology
Function and homology information


dynein heavy chain binding / positive regulation of intracellular transport / regulation of metaphase plate congression / positive regulation of spindle assembly / establishment of spindle localization / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / P-body assembly / minus-end-directed microtubule motor activity ...dynein heavy chain binding / positive regulation of intracellular transport / regulation of metaphase plate congression / positive regulation of spindle assembly / establishment of spindle localization / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / P-body assembly / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / centrosome localization / microtubule-based movement / nuclear migration / dynein intermediate chain binding / COPI-mediated anterograde transport / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / axon cytoplasm / 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 / stress granule assembly / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / regulation of mitotic spindle organization / AURKA Activation by TPX2 / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / cellular response to nerve growth factor stimulus / kinetochore / microtubule cytoskeleton organization / HCMV Early Events / Aggrephagy / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / late endosome / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Dynein 1 light intermediate chain / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / : / Dynein heavy chain, ATPase lid domain ...Dynein 1 light intermediate chain / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cytoplasmic dynein 1 light intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsUrnavicius L / Lau CK
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-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
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  • Surface view colored by radius
  • Surface level: 0.1
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  • Surface view with fitted model
  • Atomic models: PDB-6f1y
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6f1y
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4171.png

Downloads & links

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Map

FileDownload / File: emd_4171.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of C terminal half of dynein tail in complex with dynactin and BICDR1, focussed on light intermediate chain.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 600 pix.
= 804. Å		1.34 Å/pix.
x 600 pix.
= 804. Å		1.34 Å/pix.
x 600 pix.
= 804. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.19810796 - 0.31908697
Average (Standard dev.)-0.00010480791 (±0.003966631)
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-0.1980.319-0.000

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Supplemental data

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Sample components

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Entire : Two dynein tail domains bound to dynactin and BICDR1

EntireName: Two dynein tail domains bound to dynactin and BICDR1
Components
  • Complex: Two dynein tail domains bound to dynactin and BICDR1
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain
    • Protein or peptide: Cytoplasmic dynein 1 light intermediate chain 2

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Supramolecule #1: Two dynein tail domains bound to dynactin and BICDR1

SupramoleculeName: Two dynein tail domains bound to dynactin and BICDR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain

MacromoleculeName: Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.117113 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SLIESVRTYE RTCEKVEERN TISLLVAGLK KEVQALIAEG IALVWESYKL DPYVQRLAET VFNFQEKVDD LLIIEEKIDL EVRSLETCM YDHKTFSEIL NRVQKAVDDL NLHSYSNLPI WVNKLDMEIE RILGVRLQAG LRAWTQVLL(UNK) (UNK) (UNK)(UNK)(UNK) ...String:
SLIESVRTYE RTCEKVEERN TISLLVAGLK KEVQALIAEG IALVWESYKL DPYVQRLAET VFNFQEKVDD LLIIEEKIDL EVRSLETCM YDHKTFSEIL NRVQKAVDDL NLHSYSNLPI WVNKLDMEIE RILGVRLQAG LRAWTQVLL(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)LEESY SAVMGIVSEV EQYVKV (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

UniProtKB: Cytoplasmic dynein 1 heavy chain 1

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Macromolecule #2: Cytoplasmic dynein 1 light intermediate chain 2

MacromoleculeName: Cytoplasmic dynein 1 light intermediate chain 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.502941 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SSILSEVSTR ARSKLPSGKN ILVFGEDGSG KTTLMTKLQG AEHGKKGRGL EYLYLSVHDE DRDDHTRCNV WILDGDLYHK GLLKFAVSA ESLPETLVIF VADMSRPWTV MESLQKWASV LREHIDKMKI PPEKMRELER KFVKDFQDYM EPEEGCQGSP Q RRGPLTSG ...String:
SSILSEVSTR ARSKLPSGKN ILVFGEDGSG KTTLMTKLQG AEHGKKGRGL EYLYLSVHDE DRDDHTRCNV WILDGDLYHK GLLKFAVSA ESLPETLVIF VADMSRPWTV MESLQKWASV LREHIDKMKI PPEKMRELER KFVKDFQDYM EPEEGCQGSP Q RRGPLTSG SDEENVALPL GDNVLTHNLG IPVLVVCTKC DAVSVLEKEH DYRDEHLDFI QSHLRRFCLQ YGAALIYTSV KE EKNLDLL YKYIVHKTYG FHFTTPALVV EKDAVFIPAG WDNEKKIAIL HENFTTVKPE DAYEDFIVKP PVRKLVHDKE LAA EDEQVF LMKQQSLLAK Q

UniProtKB: Cytoplasmic dynein 1 light intermediate chain 2

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

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

2860


Details: Initial model low pass filtered to 50 A
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: 113987
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Details: Particle signal subtraction used to remove parts of the complex outside of the C terminal half of dynein tail domains.
Final 3D classificationSoftware - Name: RELION
Details: 3D classification focussed on light intermediate chain region without alignments

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient
Output model

PDB-6f1y:
Dynein light intermediate chain region of the dynein tail/dynactin/BICDR1 complex

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