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- PDB-8rgi: Structure of DYNLT1:DYNLT2B (TCTEX1:TCTEX1D2) heterodimer. -

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Basic information

Entry
Database: PDB / ID: 8rgi
TitleStructure of DYNLT1:DYNLT2B (TCTEX1:TCTEX1D2) heterodimer.
Components
  • Dynein light chain Tctex-type 1
  • Dynein light chain Tctex-type protein 2B
KeywordsTRANSPORT PROTEIN / dynein / cilia / intraflagellar transport / complex
Function / homology
Function and homology information


regulation of intraciliary retrograde transport / intracellular transport of viral protein in host cell / secretory vesicle / intraciliary retrograde transport / regulation of cilium assembly / dynein axonemal particle / Intraflagellar transport / dynein complex / regulation of G protein-coupled receptor signaling pathway / microtubule-dependent intracellular transport of viral material towards nucleus ...regulation of intraciliary retrograde transport / intracellular transport of viral protein in host cell / secretory vesicle / intraciliary retrograde transport / regulation of cilium assembly / dynein axonemal particle / Intraflagellar transport / dynein complex / regulation of G protein-coupled receptor signaling pathway / microtubule-dependent intracellular transport of viral material towards nucleus / cytoplasmic dynein complex / dynein intermediate chain binding / microtubule-based movement / cytoplasmic microtubule / establishment of mitotic spindle orientation / cilium assembly / cilium / negative regulation of neurogenesis / spindle / host cell / nervous system development / secretory granule lumen / ficolin-1-rich granule lumen / symbiont entry into host cell / cell division / Neutrophil degranulation / Golgi apparatus / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family
Similarity search - Domain/homology
Dynein light chain Tctex-type 1 / Dynein light chain Tctex-type protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsMukhopadhyay, A.G. / Toropova, K. / Daly, L. / Wells, J. / Vuolo, L. / Seda, M. / Jenkins, D. / Stephens, D.J. / Roberts, A.J.
Funding support United Kingdom, 8items
OrganizationGrant numberCountry
Wellcome Trust217186/Z/19/Z United Kingdom
Wellcome Trust221543/Z/20/Z United Kingdom
Royal SocietyRG170260 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P008348/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007202/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S013024/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S005390/1 United Kingdom
Wellcome Trust210585/Z/18/Z United Kingdom
CitationJournal: EMBO J / Year: 2024
Title: Structure and tethering mechanism of dynein-2 intermediate chains in intraflagellar transport.
Authors: Aakash G Mukhopadhyay / Katerina Toropova / Lydia Daly / Jennifer N Wells / Laura Vuolo / Miroslav Mladenov / Marian Seda / Dagan Jenkins / David J Stephens / Anthony J Roberts /
Abstract: Dynein-2 is a large multiprotein complex that powers retrograde intraflagellar transport (IFT) of cargoes within cilia/flagella, but the molecular mechanism underlying this function is still emerging. ...Dynein-2 is a large multiprotein complex that powers retrograde intraflagellar transport (IFT) of cargoes within cilia/flagella, but the molecular mechanism underlying this function is still emerging. Distinctively, dynein-2 contains two identical force-generating heavy chains that interact with two different intermediate chains (WDR34 and WDR60). Here, we dissect regulation of dynein-2 function by WDR34 and WDR60 using an integrative approach including cryo-electron microscopy and CRISPR/Cas9-enabled cell biology. A 3.9 Å resolution structure shows how WDR34 and WDR60 use surprisingly different interactions to engage equivalent sites of the two heavy chains. We show that cilia can assemble in the absence of either WDR34 or WDR60 individually, but not both subunits. Dynein-2-dependent distribution of cargoes depends more strongly on WDR60, because the unique N-terminal extension of WDR60 facilitates dynein-2 targeting to cilia. Strikingly, this N-terminal extension can be transplanted onto WDR34 and retain function, suggesting it acts as a flexible tether to the IFT "trains" that assemble at the ciliary base. We discuss how use of unstructured tethers represents an emerging theme in IFT train interactions.
History
DepositionDec 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynein light chain Tctex-type 1
B: Dynein light chain Tctex-type protein 2B


Theoretical massNumber of molelcules
Total (without water)28,5132
Polymers28,5132
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.149, 78.149, 112.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Dynein light chain Tctex-type 1 / Protein CW-1 / T-complex testis-specific protein 1 homolog


Mass: 12417.878 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLT1, TCTEL1, TCTEX-1, TCTEX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63172
#2: Protein Dynein light chain Tctex-type protein 2B / Tctex1 domain-containing protein 2


Mass: 16095.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLT2B, TCTEX1D2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WW35

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: DYNLT1-DYNLT2B was crystallized using the hanging-drop vapour diffusion method by mixing 1 ul of protein solution (15 mg/ml) with 1-2 ul of precipitant (1.2-1.4 M potassium sodium tartrate, ...Details: DYNLT1-DYNLT2B was crystallized using the hanging-drop vapour diffusion method by mixing 1 ul of protein solution (15 mg/ml) with 1-2 ul of precipitant (1.2-1.4 M potassium sodium tartrate, Tris pH 8-8.5) and incubating at 20 degrees Celsius. Crystals were cryo-protected in mother liquor supplemented with 25-30% glycerol and then flash frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Dec 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.02→45.68 Å / Num. obs: 24180 / % possible obs: 99.5 % / Redundancy: 6.08 % / CC1/2: 0.99 / Net I/σ(I): 14.56
Reflection shellResolution: 2.02→2.12 Å / Num. unique obs: 3754 / CC1/2: 0.265

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Processing

Software
NameVersionClassification
PHENIX1.18_3845:refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→45.68 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.2586 --
obs-23581 99.71 %
Refinement stepCycle: LAST / Resolution: 2.02→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 0 0 1832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071870
X-RAY DIFFRACTIONf_angle_d0.5642531
X-RAY DIFFRACTIONf_dihedral_angle_d22.673666
X-RAY DIFFRACTIONf_chiral_restr0.046284
X-RAY DIFFRACTIONf_plane_restr0.004323

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