[English] 日本語
Yorodumi
- PDB-8rgg: Structure of dynein-2 intermediate chain DYNC2I2 (WDR34) in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rgg
TitleStructure of dynein-2 intermediate chain DYNC2I2 (WDR34) in complex with dynein-2 heavy chain DYNC2H1.
Components
  • Cytoplasmic dynein 2 intermediate chain 1
  • Cytoplasmic dynein 2 intermediate chain 2
  • Dynein light chain 1, cytoplasmic
  • Dynein light chain roadblock-type 1
  • Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1
KeywordsTRANSPORT PROTEIN / dynein / cilia / intraflagellar transport / complex
Function / homology
Function and homology information


MGMT-mediated DNA damage reversal / positive regulation of non-motile cilium assembly / intraciliary retrograde transport / visual behavior / dynein light chain binding / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / intraciliary transport / cilium movement involved in cell motility / 9+2 motile cilium ...MGMT-mediated DNA damage reversal / positive regulation of non-motile cilium assembly / intraciliary retrograde transport / visual behavior / dynein light chain binding / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / intraciliary transport / cilium movement involved in cell motility / 9+2 motile cilium / mitocytosis / motile cilium assembly / dynein heavy chain binding / spinal cord motor neuron differentiation / Activation of BIM and translocation to mitochondria / DNA-methyltransferase activity / embryonic skeletal system morphogenesis / ciliary tip / Intraflagellar transport / DNA alkylation repair / negative regulation of nitric oxide biosynthetic process / DNA ligation / negative regulation of phosphorylation / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / protein localization to cilium / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / non-motile cilium assembly / coronary vasculature development / dynein light intermediate chain binding / positive regulation of smoothened signaling pathway / ciliary plasm / dorsal/ventral pattern formation / enzyme inhibitor activity / determination of left/right symmetry / embryonic limb morphogenesis / positive regulation of double-strand break repair / microtubule motor activity / ciliary base / Macroautophagy / dynein intermediate chain binding / microtubule-based movement / pericentriolar material / Golgi organization / spermatid development / axoneme / positive regulation of insulin secretion involved in cellular response to glucose stimulus / tertiary granule membrane / cytoskeletal motor activity / ficolin-1-rich granule membrane / cilium assembly / Hedgehog 'off' state / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Mitotic Prometaphase / forebrain development / 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 / kidney development / methyltransferase activity / RHO GTPases Activate Formins / cilium / mitotic spindle / protein processing / kinetochore / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / apical part of cell / scaffold protein binding / microtubule / cytoskeleton / protein domain specific binding / DNA repair / centrosome / apoptotic process / Neutrophil degranulation / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / enzyme binding / ATP hydrolysis activity / mitochondrion
Similarity search - Function
Cytoplasmic dynein 2 intermediate chain 1 / : / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / 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 ...Cytoplasmic dynein 2 intermediate chain 1 / : / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / 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
Methylated-DNA--protein-cysteine methyltransferase / Dynein light chain 1, cytoplasmic / Cytoplasmic dynein 2 heavy 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 Å
AuthorsMukhopadhyay, A.G. / Toropova, K. / Daly, L. / Wells, J. / Vuolo, L. / Mladenov, M. / Seda, M. / Jenkins, D. / Stephens, D.J. / Roberts, A.J.
Funding support United Kingdom, 9items
OrganizationGrant numberCountry
Wellcome Trust217186/Z/19/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
Wellcome Trust202679/Z/16/Z 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
Royal SocietyRG170260 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1
C: Cytoplasmic dynein 2 intermediate chain 1
D: Cytoplasmic dynein 2 intermediate chain 2
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


Theoretical massNumber of molelcules
Total (without water)741,3607
Polymers741,3607
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1 / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase / ...6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase / Cytoplasmic dynein 2 heavy chain / Dynein cytoplasmic heavy chain 2 / Dynein heavy chain 11 / hDHC11 / Dynein heavy chain isotype 1B


Mass: 515223.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DYNC2H1 with N-terminal SNAPf tag / Source: (gene. exp.) Homo sapiens (human) / Gene: MGMT, DYNC2H1, DHC1B, DHC2, DNCH2, DYH1B, KIAA1997 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P16455, UniProt: Q8NCM8, methylated-DNA-[protein]-cysteine S-methyltransferase
#2: Protein Cytoplasmic dynein 2 intermediate chain 1 / Dynein 2 intermediate chain 1 / 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: DYNC2I1, WDR60 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WVS4
#3: Protein Cytoplasmic dynein 2 intermediate chain 2 / Dynein 2 intermediate chain 2 / WD repeat-containing protein 34


Mass: 60639.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DYNC2I2 (also known as WDR34) with C-terminal Strep tag
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC2I2, WDR34 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96EX3
#4: 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
#5: 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.: 2
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

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Dynein-2 complex / Type: COMPLEX / Entity ID: all / 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
VitrificationCryogen name: ETHANE

-
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 defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113479 / Details: Global resolution 4.0A / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more