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- PDB-6f1u: N terminal region of dynein tail domains in complex with dynactin... -

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Basic information

Entry
Database: PDB / ID: 6f1u
TitleN terminal region of dynein tail domains in complex with dynactin filament and BICDR-1
Components
  • (Cytoplasmic dynein 1 ...) x 2
  • (Dynactin subunit ...) x 2
  • ARP1 actin related protein 1 homolog A
  • BICD family-like cargo adapter 1
  • Capping protein (Actin filament) muscle Z-line, alpha 1
  • F-actin capping protein beta subunit
KeywordsMOTOR PROTEIN / Cryo-EM / Complex / Cargo adaptor
Function / homology
Function and homology information


Golgi to secretory granule transport / RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / RHOF GTPase cycle / dynactin complex / transport along microtubule / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane ...Golgi to secretory granule transport / RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / RHOF GTPase cycle / dynactin complex / transport along microtubule / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / F-actin capping protein complex / WASH complex / Recruitment of mitotic centrosome proteins and complexes / dynein light chain binding / dynein heavy chain binding / positive regulation of intracellular transport / regulation of metaphase plate congression / positive regulation of spindle assembly / barbed-end actin filament capping / establishment of spindle localization / regulation of cell morphogenesis / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / P-body assembly / microtubule motor activity / Recruitment of NuMA to mitotic centrosomes / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / COPI-mediated anterograde transport / microtubule-based movement / nuclear migration / cortical cytoskeleton / dynein intermediate chain binding / dynactin binding / microtubule-based process / COPI-mediated anterograde transport / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / cytoskeleton organization / Mitotic Prometaphase / axon cytoplasm / 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 / sarcomere / AURKA Activation by TPX2 / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / small GTPase binding / neuron projection development / HCMV Early Events / Aggrephagy / actin filament binding / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / positive regulation of cold-induced thermogenesis / actin binding / actin cytoskeleton organization / cell cortex / vesicle / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / : / Dynamitin / Dynamitin / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site ...F-actin capping protein, alpha/beta subunit, N-terminal domain / F-actin capping protein, alpha subunit / F-actin capping protein, beta subunit / : / Dynamitin / Dynamitin / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / : / Ribosomal protein S3 C-terminal domain / 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 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Aspartate Aminotransferase, domain 1 / Actin / Actin family / Actin / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / WD domain, G-beta repeat / 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 / Alpha-Beta Complex / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BICD family-like cargo adapter 1 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 2 / Dynactin subunit 2 / Alpha-centractin / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsUrnavicius, L. / Lau, C.K. / Elshenawy, M.M. / Morales-Rios, E. / Motz, C. / Yildiz, A. / Carter, A.P.
Funding support United Kingdom, 2items
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, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
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Revision 1.1Jan 31, 2018Group: Database references / Refinement description / Category: citation / em_3d_fitting
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _em_3d_fitting.target_criteria
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: database_2 / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Revision 1.5Oct 1, 2025Group: Advisory / Data collection / Derived calculations
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Assembly

Deposited unit
B: ARP1 actin related protein 1 homolog A
D: ARP1 actin related protein 1 homolog A
F: ARP1 actin related protein 1 homolog A
K: Capping protein (Actin filament) muscle Z-line, alpha 1
L: F-actin capping protein beta subunit
c: Dynactin subunit 2
d: Dynactin subunit 2
f: Cytoplasmic dynein 1 heavy chain 1
m: Cytoplasmic dynein 1 heavy chain 1
n: Cytoplasmic dynein 1 heavy chain 1
h: Cytoplasmic dynein 1 intermediate chain 2
X: BICD family-like cargo adapter 1
x: BICD family-like cargo adapter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)810,93716
Polymers809,65513
Non-polymers1,2823
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34970 Å2
ΔGint-160 kcal/mol
Surface area171140 Å2
MethodPISA

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Components

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Protein , 4 types, 7 molecules BDFKLXx

#1: Protein ARP1 actin related protein 1 homolog A


Mass: 42670.688 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: ADP: adenosine diphosphate / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z5G5
#2: Protein Capping protein (Actin filament) muscle Z-line, alpha 1 / F-actin capping protein alpha 1 subunit / F-actin capping protein subunit alpha 1


Mass: 33059.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0PFK5
#3: Protein F-actin capping protein beta subunit / F-actin-capping protein subunit beta / F-actin-capping protein subunit beta isoform 1


Mass: 30566.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A9XFX6
#8: Protein BICD family-like cargo adapter 1 / Bicaudal D-related protein 1 / BICDR-1 / Coiled-coil domain-containing protein 64A


Mass: 65377.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bicdl1, Bicdr1, Ccdc64 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0JNT9

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Dynactin subunit ... , 2 types, 2 molecules cd

#4: Protein/peptide Dynactin subunit 2


Mass: 5581.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKF9
#5: Protein/peptide Dynactin subunit 2


Mass: 2880.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SL58, UniProt: F1SKF9*PLUS

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Cytoplasmic dynein 1 ... , 2 types, 4 molecules fmnh

#6: Protein Cytoplasmic dynein 1 heavy chain 1 / Cytoplasmic dynein heavy chain 1 / Dynein heavy chain / cytosolic


Mass: 136786.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14204
#7: Protein Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein intermediate chain 2 / Dynein intermediate chain 2 / cytosolic / DH IC-2


Mass: 68442.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1I2, DNCI2, DNCIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13409

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Non-polymers , 1 types, 3 molecules

#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Two dynein tail domains bound to dynactin and BICDR1.COMPLEX#1-#80MULTIPLE SOURCES
2dynactin filamentCOMPLEX#1-#51NATURAL
3Cytoplasmic dyneinCOMPLEX#6-#71RECOMBINANT
4BICDR1COMPLEX#81RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Sus scrofa (pig)9823
23Homo sapiens (human)9606
34Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Spodoptera frugiperda (fall armyworm)7108
24Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2919: / Classification: refinement
EM software
IDNameVersionCategory
1RELIONparticle selection
4CTFFIND3CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205611 / Symmetry type: POINT
Atomic model buildingSpace: REAL / Target criteria: Cross-correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01529461
ELECTRON MICROSCOPYf_angle_d1.57939787
ELECTRON MICROSCOPYf_dihedral_angle_d12.39317948
ELECTRON MICROSCOPYf_chiral_restr0.0794342
ELECTRON MICROSCOPYf_plane_restr0.018693

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