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- PDB-6rlb: Structure of the dynein-2 complex; tail domain -

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Basic information

Entry
Database: PDB / ID: 6rlb
TitleStructure of the dynein-2 complex; tail domain
Components
  • (Dynein light chain ...) x 2
  • (WD repeat-containing protein ...) x 2
  • Cytoplasmic dynein 2 light intermediate chain 1
  • O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein
KeywordsMOTOR PROTEIN / dynein / cilia / intraflagellar transport / complex
Function / homology
Function and homology information


intraciliary transport involved in cilium assembly / positive regulation of non-motile cilium assembly / intraciliary retrograde transport / visual behavior / organelle organization / dynein light chain binding / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / intraciliary transport / ciliary transition zone ...intraciliary transport involved in cilium assembly / positive regulation of non-motile cilium assembly / intraciliary retrograde transport / visual behavior / organelle organization / dynein light chain binding / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / intraciliary transport / ciliary transition zone / mitocytosis / dynein heavy chain binding / regulation of cilium assembly / motile cilium assembly / Activation of BIM and translocation to mitochondria / embryonic skeletal system morphogenesis / ciliary tip / DNA modification / Intraflagellar transport / negative regulation of nitric oxide biosynthetic process / negative regulation of phosphorylation / cell projection organization / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / ciliary plasm / enzyme inhibitor activity / motile cilium / determination of left/right symmetry / microtubule motor activity / ciliary base / dynein intermediate chain binding / Macroautophagy / microtubule-based movement / pericentriolar material / spermatid development / axoneme / positive regulation of insulin secretion involved in cellular response to glucose stimulus / tertiary granule membrane / ficolin-1-rich granule membrane / cilium assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / 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 / substantia nigra development / MHC class II antigen presentation / centriole / nitric-oxide synthase regulator activity / AURKA Activation by TPX2 / ciliary basal body / regulation of mitochondrial membrane potential / filopodium / RHO GTPases Activate Formins / cilium / kinetochore / mitotic spindle / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / apical part of cell / methylation / scaffold protein binding / microtubule / cytoskeleton / protein domain specific binding / DNA repair / centrosome / apoptotic process / Neutrophil degranulation / protein-containing complex binding / Golgi apparatus / enzyme binding / ATP hydrolysis activity / mitochondrion / DNA binding / extracellular space / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cytoplasmic dynein 2 light intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 1 / : / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain / Methylguanine DNA methyltransferase, ribonuclease-like domain / Dynein family light intermediate chain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Dynein light intermediate chain (DLIC) / Dynein light chain roadblock-type 1/2 / Methylated DNA-protein cysteine methyltransferase domain superfamily ...Cytoplasmic dynein 2 light intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 1 / : / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain / Methylguanine DNA methyltransferase, ribonuclease-like domain / Dynein family light intermediate chain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Dynein light intermediate chain (DLIC) / Dynein light chain roadblock-type 1/2 / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / 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, 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 / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cytoplasmic dynein 2 heavy chain 1 / Methylated-DNA--protein-cysteine methyltransferase / Dynein light chain 1, cytoplasmic / Cytoplasmic dynein 2 light intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 2 / Dynein light chain roadblock-type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsToropova, K. / Zalyte, R. / Mukhopadhyay, A.G. / Mladenov, M. / Carter, A.P. / Roberts, A.J.
Funding support United Kingdom, 8items
OrganizationGrant numberCountry
Wellcome Trust104196/Z/14/Z United Kingdom
Royal Society104196/Z/14/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P008348/1 United Kingdom
Royal SocietyRG170260 United Kingdom
Wellcome TrustWT100387 United Kingdom
Medical Research Council (United Kingdom)MC_UP_A025_1011 United Kingdom
Wellcome Trust079605/Z/06/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L014211/1 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structure of the dynein-2 complex and its assembly with intraflagellar transport trains.
Authors: Katerina Toropova / Ruta Zalyte / Aakash G Mukhopadhyay / Miroslav Mladenov / Andrew P Carter / Anthony J Roberts /
Abstract: Dynein-2 assembles with polymeric intraflagellar transport (IFT) trains to form a transport machinery that is crucial for cilia biogenesis and signaling. Here we recombinantly expressed the ~1.4-MDa ...Dynein-2 assembles with polymeric intraflagellar transport (IFT) trains to form a transport machinery that is crucial for cilia biogenesis and signaling. Here we recombinantly expressed the ~1.4-MDa human dynein-2 complex and solved its cryo-EM structure to near-atomic resolution. The two identical copies of the dynein-2 heavy chain are contorted into different conformations by a WDR60-WDR34 heterodimer and a block of two RB and six LC8 light chains. One heavy chain is steered into a zig-zag conformation, which matches the periodicity of the anterograde IFT-B train. Contacts between adjacent dyneins along the train indicate a cooperative mode of assembly. Removal of the WDR60-WDR34-light chain subcomplex renders dynein-2 monomeric and relieves autoinhibition of its motility. Our results converge on a model in which an unusual stoichiometry of non-motor subunits controls dynein-2 assembly, asymmetry, and activity, giving mechanistic insight into the interaction of dynein-2 with IFT trains and the origin of diverse functions in the dynein family.
History
DepositionMay 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein
B: O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein
C: WD repeat-containing protein 60
D: WD repeat-containing protein 34
E: Cytoplasmic dynein 2 light intermediate chain 1
F: Cytoplasmic dynein 2 light intermediate chain 1
G: Dynein light chain roadblock-type 1
H: Dynein light chain roadblock-type 1
I: Dynein light chain 1, cytoplasmic
J: Dynein light chain 1, cytoplasmic
K: Dynein light chain 1, cytoplasmic
L: Dynein light chain 1, cytoplasmic
M: Dynein light chain 1, cytoplasmic
N: Dynein light chain 1, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)1,377,60314
Polymers1,377,60314
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 4 molecules ABEF

#1: Protein O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein


Mass: 515223.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: E5BBQ0, UniProt: B0I1S0
#4: Protein Cytoplasmic dynein 2 light intermediate chain 1 / Dynein 2 light intermediate chain


Mass: 39681.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC2LI1, D2LIC, LIC3, CGI-60 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TCX1

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WD repeat-containing protein ... , 2 types, 2 molecules CD

#2: Protein WD repeat-containing protein 60


Mass: 122865.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR60 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WVS4
#3: Protein WD repeat-containing protein 34


Mass: 60768.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR34 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96EX3

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Dynein light chain ... , 2 types, 8 molecules GHIJKLMN

#5: Protein Dynein light chain roadblock-type 1 / Bithoraxoid-like protein / BLP / Dynein light chain 2A / cytoplasmic / Dynein-associated protein ...Bithoraxoid-like protein / BLP / Dynein light chain 2A / cytoplasmic / Dynein-associated protein Km23 / Roadblock domain-containing protein 1


Mass: 10934.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLRB1, BITH, DNCL2A, DNLC2A, ROBLD1, HSPC162 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NP97
#6: Protein
Dynein light chain 1, cytoplasmic / 8 kDa dynein light chain / DLC8 / Dynein light chain LC8-type 1 / Protein inhibitor of neuronal ...8 kDa dynein light chain / DLC8 / Dynein light chain LC8-type 1 / Protein inhibitor of neuronal nitric oxide synthase / PIN


Mass: 10381.899 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLL1, DLC1, DNCL1, DNCLC1, HDLC1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63167

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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

ComponentName: Dynein-2 complex; tail domain / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Dynein-2 complex; tail domain
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Details: Average electron dose per image (e-/A2) for additional datasets was 46.8 and 45.4
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
4GctfCTF correction
5RELION2.1CTF correction
11RELION2.1initial Euler assignment
12RELION2.1final Euler assignment
14RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68623 / Symmetry type: POINT

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