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- EMDB-19132: Structure of dynein-2 intermediate chain DYNC2I2 (WDR34) in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-19132
TitleStructure of dynein-2 intermediate chain DYNC2I2 (WDR34) in complex with dynein-2 heavy chain DYNC2H1.
Map dataLocally refined map, locally sharpened with locscale
Sample
  • Complex: Dynein-2 complex
    • Protein or peptide: Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1
    • Protein or peptide: Cytoplasmic dynein 2 intermediate chain 1
    • Protein or peptide: Cytoplasmic dynein 2 intermediate chain 2
    • Protein or peptide: Dynein light chain roadblock-type 1
    • Protein or peptide: Dynein light chain 1, cytoplasmic
Keywordsdynein / cilia / intraflagellar transport / complex / TRANSPORT PROTEIN
Function / homology
Function and homology information


MGMT-mediated DNA damage reversal / nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / deoxyribonuclease inhibitor activity / visual behavior / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / intraciliary retrograde transport / cilium movement involved in cell motility / 9+2 motile cilium ...MGMT-mediated DNA damage reversal / nitric-oxide synthase inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / deoxyribonuclease inhibitor activity / visual behavior / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / intraciliary retrograde transport / cilium movement involved in cell motility / 9+2 motile cilium / intraciliary transport / dynein light chain binding / dynein heavy chain binding / motile cilium assembly / spinal cord motor neuron differentiation / DNA-methyltransferase activity / Activation of BIM and translocation to mitochondria / embryonic skeletal system morphogenesis / negative regulation of phosphorylation / ciliary tip / Intraflagellar transport / negative regulation of nitric oxide biosynthetic process / dynein complex / : / coronary vasculature development / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / non-motile cilium assembly / DNA alkylation repair / cytoplasmic dynein complex / protein localization to cilium / 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 / microtubule motor activity / positive regulation of double-strand break repair / ciliary base / dynein intermediate chain binding / microtubule-based movement / Macroautophagy / pericentriolar material / Golgi organization / positive regulation of insulin secretion involved in cellular response to glucose stimulus / axoneme / cytoskeletal motor activity / tertiary granule membrane / ficolin-1-rich granule membrane / spermatid development / cilium assembly / Hedgehog 'off' state / 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 / forebrain development / 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 / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / substantia nigra development / AURKA Activation by TPX2 / centriole / ciliary basal body / filopodium / methyltransferase activity / kidney development / RHO GTPases Activate Formins / cilium / mitotic spindle / protein processing / 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 / negative regulation of apoptotic process / apoptotic process / Golgi apparatus / enzyme binding / ATP hydrolysis activity
Similarity search - Function
Cytoplasmic dynein 2 intermediate chain 1 / : / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain / 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 ...Cytoplasmic dynein 2 intermediate chain 1 / : / Cytoplasmic dynein 2 heavy chain 1, AAA+ ATPase domain / 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 / 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 / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsMukhopadhyay AG / Toropova K / Daly L / Wells J / Vuolo L / Mladenov M / Seda M / Jenkins D / Stephens DJ / Roberts AJ
Funding support United Kingdom, 9 items
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, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19132.png

Downloads & links

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Map

FileDownload / File: emd_19132.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally refined map, locally sharpened with locscale
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 248.4 Å		0.83 Å/pix.
x 300 pix.
= 248.4 Å		0.83 Å/pix.
x 300 pix.
= 248.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
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Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.22609186 - 0.6717438
Average (Standard dev.)0.0017916329 (±0.017048597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 248.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19132_msk_1.map
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Additional map: Locally refined map, unsharpened

Fileemd_19132_additional_1.map
AnnotationLocally refined map, unsharpened
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Additional map: Globally refined map, unsharpened

Fileemd_19132_additional_2.map
AnnotationGlobally refined map, unsharpened
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Additional map: Composite map of locally refined WDR34 and WDR60 map regions.

Fileemd_19132_additional_3.map
AnnotationComposite map of locally refined WDR34 and WDR60 map regions.
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Half map: #2

Fileemd_19132_half_map_1.map
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Half map: #1

Fileemd_19132_half_map_2.map
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Sample components

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Entire : Dynein-2 complex

EntireName: Dynein-2 complex
Components
  • Complex: Dynein-2 complex
    • Protein or peptide: Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1
    • Protein or peptide: Cytoplasmic dynein 2 intermediate chain 1
    • Protein or peptide: Cytoplasmic dynein 2 intermediate chain 2
    • Protein or peptide: Dynein light chain roadblock-type 1
    • Protein or peptide: Dynein light chain 1, cytoplasmic

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Supramolecule #1: Dynein-2 complex

SupramoleculeName: Dynein-2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dy...

MacromoleculeName: Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1
type: protein_or_peptide / ID: 1 / Details: DYNC2H1 with N-terminal SNAPf tag / Number of copies: 1 / Enantiomer: LEVO
EC number: methylated-DNA-[protein]-cysteine S-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 515.223031 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GDKDCEMKRT TLDSPLGKLE LSGCEQGLHR IIFLGKGTSA ADAVEVPAPA AVLGGPEPLM QATAWLNAYF HQPEAIEEFP VPALHHPVF QQESFTRQVL WKLLKVVKFG EVISYSHLAA LAGNPAATAA VKTALSGNPV PILIPCHRVV QGDLDVGGYE G GLAVKEWL ...String:
GDKDCEMKRT TLDSPLGKLE LSGCEQGLHR IIFLGKGTSA ADAVEVPAPA AVLGGPEPLM QATAWLNAYF HQPEAIEEFP VPALHHPVF QQESFTRQVL WKLLKVVKFG EVISYSHLAA LAGNPAATAA VKTALSGNPV PILIPCHRVV QGDLDVGGYE G GLAVKEWL LAHEGHRLGK PGLGGSLEVL FQGPDYDIPT TLEVLFQGPA NGTADVRKLF IFTTTQNYFG LMSELWDQPL LC NCLEINN FLDDGNQMLL RVQRSDAGIS FSNTIEFGDT KDKVLVFFKL RPEVITDENL HDNILVSSML ESPISSLYQA VRQ VFAPML LKDQEWSRNF DPKLQNLLSE LEAGLGIVLR RSDTNLTKLK FKEDDTRGIL TPSDEFQFWI EQAHRGNKQI SKER ANYFK ELFETIAREF YNLDSLSLLE VVDLVETTQD VVDDVWRQTE HDHYPESRML HLLDIIGGSF GRFVQKKLGT LNLWE DPYY LVKESLKAGI SICEQWVIVC NHLTGQVWQR YVPHPWKNEK YFPETLDKLG KRLEEVLAIR TIHEKFLYFL PASEEK IIC LTRVFEPFTG LNPVQYNPYT EPLWKAAVSQ YEKIIAPAEQ KIAGKLKNYI SEIQDSPQQL LQAFLKYKEL VKRPTIS KE LMLERETLLA RLVDSIKDFR LDFENRCRGI PGDASGPLSG KNLSEVVNSI VWVRQLELKV DDTIKIAEAL LSDLPGFR C FHQSAKDLLD QLKLYEQEQF DDWSRDIQSG LSDSRSGLCI EASSRIMELD SNDGLLKVHY SDRLVILLRE VRQLSALGF VIPAKIQQVA NIAQKFCKQA IILKQVAHFY NSIDQQMIQS QRPMMLQSAL AFEQIIKNSK AGSGGKSQIT WDNPKELEGY IQKLQNAAE RLATENRKLR KWHTTFCEKV VVLMNIDLLR QQQRWKDGLQ ELRTGLATVE AQGFQASDMH AWKQHWNHQL Y KALEHQYQ MGLEALNENL PEINIDLTYK QGRLQFRPPF EEIRAKYYRE MKRFIGIPNQ FKGVGEAGDE SIFSIMIDRN AS GFLTIFS KAEDLFRRLS AVLHQHKEWI VIGQVDMEAL VEKHLFTVHD WEKNFKALKI KGKEVERLPS AVKVDCLNIN CNP VKTVID DLIQKLFDLL VLSLKKSIQA HLHEIDTFVT EAMEVLTIMP QSVEEIGDAN LQYSKLQERK PEILPLFQEA EDKN RLLRT VAGGGLETIS NLKAKWDKFE LMMESHQLMI KDQIEVMKGN VKSRLQIYYQ ELEKFKARWD QLKPGDDVIE TGQHN TLDK SAKLIKEKKI EFDDLEVTRK KLVDDCHHFR LEEPNFSLAS SISKDIESCA QIWAFYEEFQ QGFQEMANED WITFRT KTY LFEEFLMNWH DRLRKVEEHS VMTVKLQSEV DKYKIVIPIL KYVRGEHLSP DHWLDLFRLL GLPRGTSLEK LLFGDLL RV ADTIVAKAAD LKDLNSRAQG EVTIREALRE LDLWGVGAVF TLIDYEDSQS RTMKLIKDWK DIVNQVGDNR CLLQSLKD S PYYKGFEDKV SIWERKLAEL DEYLQNLNHI QRKWVYLEPI FGRGALPKEQ TRFNRVDEDF RSIMTDIKKD NRVTTLTTH AGIRNSLLTI LDQLQRCQRS LNEFLEEKRS AFPRFYFIGD DDLLEILGQS TNPSVIQSHL KKLFAGINSV CFDEKSKHIT AMKSLEGEV VPFKNKVPLS NNVETWLNDL ALEMKKTLEQ LLKECVTTGR SSQGAVDPSL FPSQILCLAE QIKFTEDVEN A IKDHSLHQ IETQLVNKLE QYTNIDTSSE DPGNTESGIL ELKLKALILD IIHNIDVVKQ LNQIQVHTTE DWAWKKQLRF YM KSDHTCC VQMVDSEFQY TYEYQGNASK LVYTPLTDKC YLTLTQAMKM GLGGNPYGPA GTGKTESVKA LGGLLGRQVL VFN CDEGID VKSMGRIFVG LVKCGAWGCF DEFNRLEESV LSAVSMQIQT IQDALKNHRT VCELLGKEVE VNSNSGIFIT MNPA GKGYG GRQKLPDNLK QLFRPVAMSH PDNELIAEVI LYSEGFKDAK VLSRKLVAIF NLSRELLTPQ QHYDWGLRAL KTVLR GSGN LLRQLNKSGT TQNANESHIV VQALRLNTMS KFTFTDCTRF DALIKDVFPG IELKEVEYDE LSAALKQVFE EANYEI IPN QIKKALELYE QLCQRMGVVI VGPSGAGKST LWRMLRAALC KTGKVVKQYT MNPKAMPRYQ LLGHIDMDTR EWSDGVL TN SARQVVREPQ DVSSWIICDG DIDPEWIESL NSVLDDNRLL TMPSGERIQF GPNVNFVFET HDLSCASPAT ISRMGMIF L SDEETDLNSL IKSWLRNQPA EYRNNLENWI GDYFEKALQW VLKQNDYVVE TSLVGTVMNG LSHLHGCRDH DEFIINLIR GLGGNLNMKS RLEFTKEVFH WARESPPDFH KPMDTYYDST RGRLATYVLK KPEDLTADDF SNGLTLPVIQ TPDMQRGLDY FKPWLSSDT KQPFILVGPE GCGKGMLLRY AFSQLRSTQI ATVHCSAQTT SRHLLQKLSQ TCMVISTNTG RVYRPKDCER L VLYLKDIN LPKLDKWGTS TLVAFLQQVL TYQGFYDENL EWVGLENIQI VASMSAGGRL GRHKLTTRFT SIVRLCSIDY PE REQLQTI YGAYLEPVLH KNLKNHSIWG SSSKIYLLAG SMVQVYEQVR AKFTVDDYSH YFFTPCILTQ WVLGLFRYDL EGG SSNHPL DYVLEIVAYE ARRLFRDKIV GAKELHLFDI ILTSVFQGDW GSDILDNMSD SFYVTWGARH NSGARAAPGQ PLPP HGKPL GKLNSTDLKD VIKKGLIHYG RDNQNLDILL FHEVLEYMSR IDRVLSFPGG SLLLAGRSGV GRRTITSLVS HMHGA VLFS PKISRGYELK QFKNDLKHVL QLAGIEAQQV VLLLEDYQFV HPTFLEMINS LLSSGEVPGL YTLEELEPLL LPLKDQ ASQ DGFFGPVFNY FTYRIQQNLH IVLIMDSANS NFMINCESNP ALHKKCQVLW MEGWSNSSMK KIPEMLFSET GGGEKYN DK KRKEEKKKNS VDPDFLKSFL LIHESCKAYG ATPSQYMTFL HVYSAISSSK KKELLKRQSH LQAGVSKLNE AKALVDEL N RKAGEQSVLL KTKQDEADAA LQMITVSMQD ASEQKTELER LKHRIAEEVV KIEERKNKID DELKEVQPLV NEAKLAVGN IKPESLSEIR SLRMPPDVIR DILEGVLRLM GIFDTSWVSM KSFLAKRGVR EDIATFDARN ISKEIRESVE ELLFKNKGSF DPKNAKRAS TAAAPLAAWV KANIQYSHVL ERIHPLETEQ AGLESNLKKT EDRKRKLEEL LNSVGQKVSE LKEKFQSRTS E AAKLEAEV SKAQETIKAA EVLINQLDRE HKRWNAQVVE ITEELATLPK RAQLAAAFIT YLSAAPESLR KTCLEEWTKS AG LEKFDLR RFLCTESEQL IWKSEGLPSD DLSIENALVI LQSRVCPFLI DPSSQATEWL KTHLKDSRLE VINQQDSNFI TAL ELAVRF GKTLIIQEMD GVEPVLYPLL RRDLVAQGPR YVVQIGDKII DYNEEFRLFL STRNPNPFIP PDAASIVTEV NFTT TRSGL RGQLLALTIQ HEKPDLEEQK TKLLQQEEDK KIQLAKLEES LLETLATSQG NILENKDLIE SLNQTKASSA LIQES LKES YKLQISLDQE RDAYLPLAES ASKMYFIISD LSKINNMYRF SLAAFLRLFQ RALQNKQDSE NTEQRIQSLI SSLQHM VYE YICRCLFKAD QLMFALHFVR GMHPELFQEN EWDTFTGVVV GDMLRKADSQ QKIRDQLPSW IDQERSWAVA TLKIALP SL YQTLCFEDAA LWRTYYNNSM CEQEFPSILA KKVSLFQQIL VVQVLRPDRL QSAMALFACK TLGLKEVSPL PLNLKRLY K ETLEIEPILI IISPGADPSQ ELQELANAER SGECYHQVAM GQGQADLAIQ MLKECARNGD WLCLKNLHLV VSWLPVLEK ELNTLQPKDT FRLWLTAEVH PNFTPILLQS SLKITYESPP GLKKNLMRTY ESWTPEQISK KDNTHRAHAL FSLAWFHAAC QERRNYIPQ GWTKFYEFSL SDLRAGYNII DRLFDGAKDV QWEFVHGLLE NAIYGGRIDN YFDLRVLQSY LKQFFNSSVI D VFNQRNKK SIFPYSVSLP QSCSILDYRA VIEKIPEDDK PSFFGLPANI ARSSQRMISS QVISQLRILG RSITAGSKFD RE IWSNELS PVLNLWKKLN QNSNLIHQKV PPPNDRQGSP ILSFIILEQF NAIRLVQSVH QSLAALSKVI RGTTLLSSEV QKL ASALLN QKCPLAWQSK WEGPEDPLQY LRGLVARALA IQNWVDKAEK QALLSETLDL SELFHPDTFL NALRQETARA VGRS VDSLK FVASWKGRLQ EAKLQIKISG LLLEGCSFDG NQLSENQLDS PSVSSVLPCF MGWIPQDACG PYSPDECISL PVYTS AERD RVVTNIDVPC GGNQDQWIQC GAALFLKNQ

UniProtKB: Methylated-DNA--protein-cysteine methyltransferase, Cytoplasmic dynein 2 heavy chain 1

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Macromolecule #2: Cytoplasmic dynein 2 intermediate chain 1

MacromoleculeName: Cytoplasmic dynein 2 intermediate chain 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 122.865156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEPGKRRTKD DTWKADDLRK HLWAIQSGGS KEERKHREKK LRKESEMDLP EHKEPRCRDP DQDARSRDRV AEVHTAKESP RGERDRDRQ RERRRDAKDR EKEKLKEKHR EAEKSHSRGK DREKEKDRRA RKEELRQTVA HHNLLGQETR DRQLLERAER K GRSVSKVR ...String:
MEPGKRRTKD DTWKADDLRK HLWAIQSGGS KEERKHREKK LRKESEMDLP EHKEPRCRDP DQDARSRDRV AEVHTAKESP RGERDRDRQ RERRRDAKDR EKEKLKEKHR EAEKSHSRGK DREKEKDRRA RKEELRQTVA HHNLLGQETR DRQLLERAER K GRSVSKVR SEEKDEDSER GDEDRERRYR ERKLQYGDSK DNPLKYWLYK EEGERRHRKP REPDRDKKHR EKSSTREKRE KY SKEKSNS FSDKGEERHK EKRHKEGFHF DDERHQSNVD RKEKSAKDEP RKREFQNGEH RNRGASSKRD GTSSQHAENL VRN HGKDKD SRRKHGHEEG SSVWWKLDQR PGGEETVEIE KEETDLENAR ADAYTASCED DFEDYEDDFE VCDGDDDESS NEPE SREKL EELPLAQKKE IQEIQRAINA ENERIGELSL KLFQKRGRTE FEKEPRTDTN SSPSRASVCG IFVDFASASH RQKSR TQAL KQKMRSTKLL RLIDLDFSFT FSLLDLPPVN EYDMYIRNFG KKNTKQAYVQ CNEDNVERDI QTEEIETREV WTQHPG EST VVSGGSEQRD TSDAVVMPKI DTPRLCSFLR AACQVMAVLL EEDRLAAEPS WNLRAQDRAL YFSDSSSQLN TSLPFLQ NR KVSSLHTSRV QRQMVVSVHD LPEKSFVPLL DSKYVLCVWD IWQPSGPQKV LICESQVTCC CLSPLKAFLL FAGTAHGS V VVWDLREDSR LHYSVTLSDG FWTFRTATFS TDGILTSVNH RSPLQAVEPI STSVHKKQSF VLSPFSTQEE MSGLSFHIA SLDESGVLNV WVVVELPKAD IAGSISDLGL MPGGRVKLVH SALIQLGDSL SHKGNEFWGT TQTLNVKFLP SDPNHFIIGT DMGLISHGT RQDLRVAPKL FKPQQHGIRP VKVNVIDFSP FGEPIFLAGC SDGSIRLHQL SSAFPLLQWD SSTDSHAVTG L QWSPTRPA VFLVQDDTSN IYIWDLLQSD LGPVAKQQVS PNRLVAMAAV GEPEKAGGSF LALVLARASG SIDIQHLKRR WA APEVDEC NRLRLLLQEA LWPEGKLHK

UniProtKB: Cytoplasmic dynein 2 intermediate chain 1

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Macromolecule #3: Cytoplasmic dynein 2 intermediate chain 2

MacromoleculeName: Cytoplasmic dynein 2 intermediate chain 2 / type: protein_or_peptide / ID: 3
Details: DYNC2I2 (also known as WDR34) with C-terminal Strep tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.639129 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MATRAQPGPL SQAGSAGVAA LATVGVASGP GPGRPGPLQD ETLGVASVPS QWRAVQGIRG ETKSCQTASI ATASASAQAR NHVDAQVQT EAPVPVSVQP PSQYDIPRLA AFLRRVEAMV IRELNKNWQS HAFDGFEVNW TEQQQMVSCL YTLGYPPAQA Q GLHVTSIS ...String:
MATRAQPGPL SQAGSAGVAA LATVGVASGP GPGRPGPLQD ETLGVASVPS QWRAVQGIRG ETKSCQTASI ATASASAQAR NHVDAQVQT EAPVPVSVQP PSQYDIPRLA AFLRRVEAMV IRELNKNWQS HAFDGFEVNW TEQQQMVSCL YTLGYPPAQA Q GLHVTSIS WNSTGSVVAC AYGRLDHGDW STLKSFVCAW NLDRRDLRPQ QPSAVVEVPS AVLCLAFHPT QPSHVAGGLY SG EVLVWDL SRLEDPLLWR TGLTDDTHTD PVSQVVWLPE PGHSHRFQVL SVATDGKVLL WQGIGVGQLQ LTEGFALVMQ QLP RSTKLK KHPRGETEVG ATAVAFSSFD PRLFILGTEG GFPLKCSLAA GEAALTRMPS SVPLRAPAQF TFSPHGGPIY SVSC SPFHR NLFLSAGTDG HVHLYSMLQA PPLTSLQLSL KYLFAVRWSP VRPLVFAAAS GKGDVQLFDL QKSSQKPTVL IKQTQ DESP VYCLEFNSQQ TQLLAAGDAQ GTVKVWQLST EFTEQGPREA EDLDCLAAEV AAWSHPQFEK GSAGSAAGSG AGWSHP QFE K

UniProtKB: Cytoplasmic dynein 2 intermediate chain 2

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Macromolecule #4: Dynein light chain roadblock-type 1

MacromoleculeName: Dynein light chain roadblock-type 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.934576 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAEVEETLKR LQSQKGVQGI IVVNTEGIPI KSTMDNPTTT QYASLMHSFI LKARSTVRDI DPQNDLTFLR IRSKKNEIMV APDKDYFLI VIQNPTE

UniProtKB: Dynein light chain roadblock-type 1

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Macromolecule #5: Dynein light chain 1, cytoplasmic

MacromoleculeName: Dynein light chain 1, cytoplasmic / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.381899 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MCDRKAVIKN ADMSEEMQQD SVECATQALE KYNIEKDIAA HIKKEFDKKY NPTWHCIVGR NFGSYVTHET KHFIYFYLGQ VAILLFKSG

UniProtKB: Dynein light chain 1, cytoplasmic

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Global resolution 4.0A / Number images used: 113479
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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