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- PDB-6sc2: Structure of the dynein-2 complex; IFT-train bound model -

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Entry
Database: PDB / ID: 6sc2
TitleStructure of the dynein-2 complex; IFT-train bound model
Components
  • (Dynein light chain ...) x 2
  • (O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein,O6-alkylguanine-DNA ...) x 2
  • (WD repeat-containing protein ...) x 2
  • Cytoplasmic dynein 2 light intermediate chain 1
KeywordsMOTOR PROTEIN / dynein / cilia / intraflagellar transport / complex
Function / homology
Function and homology information


intraciliary transport involved in cilium assembly / nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / deoxyribonuclease inhibitor activity / visual behavior / intraciliary retrograde transport / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / intraciliary transport / dynein light chain binding ...intraciliary transport involved in cilium assembly / nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / deoxyribonuclease inhibitor activity / visual behavior / intraciliary retrograde transport / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / intraciliary transport / dynein light chain binding / ciliary transition zone / dynein heavy chain binding / regulation of cilium assembly / motile cilium assembly / Activation of BIM and translocation to mitochondria / embryonic skeletal system morphogenesis / ciliary tip / negative regulation of phosphorylation / Intraflagellar transport / negative regulation of nitric oxide biosynthetic process / dynein complex / cell projection organization / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / ciliary plasm / motile cilium / enzyme inhibitor activity / determination of left/right symmetry / microtubule motor activity / ciliary base / dynein intermediate chain binding / Macroautophagy / pericentriolar material / microtubule-based movement / positive regulation of insulin secretion involved in cellular response to glucose stimulus / axoneme / tertiary granule membrane / ficolin-1-rich granule membrane / spermatid development / cilium assembly / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / EML4 and NUDC in mitotic spindle formation / Recruitment of mitotic centrosome proteins and complexes / axon cytoplasm / 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 / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / substantia nigra development / centriole / AURKA Activation by TPX2 / ciliary basal body / filopodium / RHO GTPases Activate Formins / cilium / mitotic spindle / kinetochore / HCMV Early Events / Aggrephagy / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / apical part of cell / site of double-strand break / scaffold protein binding / methylation / microtubule / cytoskeleton / DNA repair / centrosome / DNA damage response / Neutrophil degranulation / protein-containing complex binding / apoptotic process / Golgi apparatus / enzyme binding / ATP hydrolysis activity / mitochondrion / DNA binding / extracellular space / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / 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 / Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Dynein light chain roadblock-type 1/2 / Methylguanine DNA methyltransferase, ribonuclease-like domain ...Cytoplasmic dynein 2 light intermediate chain 1 / Cytoplasmic dynein 2 intermediate chain 1 / : / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain / Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Dynein light chain roadblock-type 1/2 / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / 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 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / Dynein light chain 2a, cytoplasmic / 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 / : / Dynein heavy chain, ATPase lid domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / 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 / Beta-Lactamase / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 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: 3.9 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
Citation
Journal: 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.
#1: Journal: Nat Cell Biol / Year: 2018
Title: The cryo-EM structure of intraflagellar transport trains reveals how dynein is inactivated to ensure unidirectional anterograde movement in cilia.
Authors: Mareike A Jordan / Dennis R Diener / Ludek Stepanek / Gaia Pigino /
Abstract: Movement of cargos along microtubules plays key roles in diverse cellular processes, from signalling to mitosis. In cilia, rapid movement of ciliary components along the microtubules to and from the ...Movement of cargos along microtubules plays key roles in diverse cellular processes, from signalling to mitosis. In cilia, rapid movement of ciliary components along the microtubules to and from the assembly site is essential for the assembly and disassembly of the structure itself. This bidirectional transport, known as intraflagellar transport (IFT), is driven by the anterograde motor kinesin-2 and the retrograde motor dynein-1b (dynein-2 in mammals). However, to drive retrograde transport, dynein-1b must first be delivered to the ciliary tip by anterograde IFT. Although, the presence of opposing motors in bidirectional transport processes often leads to periodic stalling and slowing of cargos, IFT is highly processive. Using cryo-electron tomography, we show that a tug-of-war between kinesin-2 and dynein-1b is prevented by loading dynein-1b onto anterograde IFT trains in an autoinhibited form and by positioning it away from the microtubule track to prevent binding. Once at the ciliary tip, dynein-1b must transition into an active form and engage microtubules to power retrograde trains. These findings provide a striking example of how coordinated structural changes mediate the behaviour of complex cellular machinery.
History
DepositionJul 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2May 15, 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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Assembly

Deposited unit
A: O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein,O6-alkylguanine-DNA alkyltransferase mutant,Cytoplasmic dynein 2 heavy chain 1,DYNC2H1 variant protein,DYNC2H1 variant protein,DYNC2H1 variant protein
B: O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein,O6-alkylguanine-DNA alkyltransferase mutant,Cytoplasmic dynein 2 heavy chain 1,DYNC2H1 variant protein,DYNC2H1 variant protein,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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,363,28524
Polymers1,359,65914
Non-polymers3,62610
Water00
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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O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein,O6-alkylguanine-DNA ... , 2 types, 2 molecules AB

#1: Protein O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein,O6-alkylguanine-DNA alkyltransferase mutant,Cytoplasmic dynein 2 heavy chain 1,DYNC2H1 variant protein,DYNC2H1 variant protein,DYNC2H1 variant protein


Mass: 507610.219 Da / Num. of mol.: 1
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
#2: Protein O6-alkylguanine-DNA alkyltransferase mutant,DYNC2H1 variant protein,O6-alkylguanine-DNA alkyltransferase mutant,Cytoplasmic dynein 2 heavy chain 1,DYNC2H1 variant protein,DYNC2H1 variant protein,DYNC2H1 variant protein


Mass: 504891.344 Da / Num. of mol.: 1
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

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

#3: 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
#4: 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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Protein , 1 types, 2 molecules EF

#5: 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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Dynein light chain ... , 2 types, 8 molecules GHIJKLMN

#6: 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
#7: 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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Non-polymers , 3 types, 10 molecules

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


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#9: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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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 / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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
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 FIELD / 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 QUANTUM (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
2EPUimage acquisition
4GctfCTF correction
5RELION2.1CTF correction
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57265
Details: Above values for the motor domain map (EMD-4917). For the tail domain map (EMD-4918), number of particles used was 68623, resolution was 4.5 A using the FSC 0.143 cut-off, even/odd maps ...Details: Above values for the motor domain map (EMD-4917). For the tail domain map (EMD-4918), number of particles used was 68623, resolution was 4.5 A using the FSC 0.143 cut-off, even/odd maps refined totally independent (gold standard), C1 symmetry.
Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE
Details: EMD entries 4917 and 4918 (motor and tail domain reconstructions of human dynein-2 complex) were docked into a subtomogram average of IFT complex B and inhibited dynein-1b in anterograde IFT ...Details: EMD entries 4917 and 4918 (motor and tail domain reconstructions of human dynein-2 complex) were docked into a subtomogram average of IFT complex B and inhibited dynein-1b in anterograde IFT trains from C. reinhardtii cilia (EMD-4303) using Chimera's 'Fit in Map' command. The two DHC2 bundles connecting the tail and motor domain were modelled using SWISS-MODEL and RaptorX Contact (deposition as UNK).

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