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- EMDB-73175: Motor domain of human dynein-1 in pre-power stroke bound to dynac... -

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Basic information

Entry
Database: EMDB / ID: EMD-73175
TitleMotor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B-ICD and LIS1
Map dataSharpened map of motor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B-ICD and LIS1
Sample
  • Complex: Motor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B-ICD and LIS1
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
    • Protein or peptide: Platelet-activating factor acetylhydrolase IB subunit beta
    • Protein or peptide: Cytoplasmic dynein 1 intermediate chain 2
    • Protein or peptide: Dynactin subunit 1
    • Protein or peptide: Dynein light chain 1, cytoplasmic
    • Protein or peptide: Dynein light chain Tctex-type 1
    • Protein or peptide: Cytoplasmic dynein 1 light intermediate chain 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsDynein-1 / Lis1 / p150glued / MOTOR PROTEIN
Function / homology
Function and homology information


intracellular transport of viral protein in host cell / nitric-oxide synthase inhibitor activity / cell cortex region / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / negative regulation of DNA strand resection involved in replication fork processing / secretory vesicle / corpus callosum morphogenesis ...intracellular transport of viral protein in host cell / nitric-oxide synthase inhibitor activity / cell cortex region / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / negative regulation of DNA strand resection involved in replication fork processing / secretory vesicle / corpus callosum morphogenesis / centriolar subdistal appendage / negative regulation of phosphorylation / maintenance of centrosome location / centriole-centriole cohesion / intraciliary retrograde transport / platelet activating factor metabolic process / positive regulation of neuromuscular junction development / radial glia-guided pyramidal neuron migration / microtubule anchoring at centrosome / establishment of centrosome localization / acrosome assembly / cerebral cortex neuron differentiation / nuclear membrane disassembly / central region of growth cone / maintenance of synapse structure / dynein light chain binding / microtubule sliding / transport along microtubule / ventral spinal cord development / dynein heavy chain binding / motile cilium assembly / Activation of BIM and translocation to mitochondria / positive regulation of cytokine-mediated signaling pathway / microtubule organizing center organization / positive regulation of embryonic development / layer formation in cerebral cortex / interneuron migration / mitotic nuclear membrane disassembly / dynein complex / astral microtubule / auditory receptor cell development / microtubule plus-end / cortical microtubule organization / positive regulation of microtubule nucleation / XBP1(S) activates chaperone genes / Intraflagellar transport / myeloid leukocyte migration / reelin-mediated signaling pathway / positive regulation of intracellular transport / regulation of metaphase plate congression / positive regulation of spindle assembly / positive regulation of dendritic spine morphogenesis / melanosome transport / osteoclast development / negative regulation of nitric oxide biosynthetic process / establishment of spindle localization / regulation of G protein-coupled receptor signaling pathway / stereocilium / microtubule plus-end binding / brain morphogenesis / microtubule-dependent intracellular transport of viral material towards nucleus / non-motile cilium assembly / motile cilium / vesicle transport along microtubule / retrograde transport, endosome to Golgi / retrograde axonal transport / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / microtubule associated complex / negative regulation of JNK cascade / centrosome localization / P-body assembly / dynein light intermediate chain binding / cytoplasmic dynein complex / microtubule motor activity / kinesin complex / neuromuscular process controlling balance / stem cell division / microtubule-based movement / nuclear migration / perinuclear theca / neuromuscular process / Macroautophagy / establishment of mitotic spindle orientation / neuromuscular junction development / dynein intermediate chain binding / motor behavior / cell leading edge / germ cell development / transmission of nerve impulse / dynein complex binding / tertiary granule membrane / neuroblast proliferation / dynactin binding / cochlea development / ficolin-1-rich granule membrane / protein secretion / spermatid development / microtubule-based process / positive regulation of axon extension
Similarity search - Function
: / : / PAC1 LisH domain / Dynein associated protein / Dynein associated protein / Dynein 1 light intermediate chain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein family light intermediate chain ...: / : / PAC1 LisH domain / Dynein associated protein / Dynein associated protein / Dynein 1 light intermediate chain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein regulator LIS1 / LIS1, N-terminal / 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 / : / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Lissencephaly type-1-like homology motif / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / : / Dynein heavy chain, ATPase lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / 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 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing 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
Cytoplasmic dynein 1 light intermediate chain 2 / Platelet-activating factor acetylhydrolase IB subunit beta / Dynein light chain 1, cytoplasmic / Dynein light chain Tctex-type 1 / Cytoplasmic dynein 1 intermediate chain 2 / Dynactin subunit 1 / Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.46 Å
AuthorsYang J / Rao Q / Chai P / Zhang K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM142959 United States
CitationJournal: Nature / Year: 2026
Title: Roles of microtubules and LIS1 in dynein transport machinery assembly.
Authors: Qinhui Rao / Jun Yang / Pengxin Chai / Steven Markus / Kai Zhang /
Abstract: Cytoplasmic dynein-1, a microtubule (MT)-based motor protein, requires dynactin and a coiled-coil adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The roles of MTs and dynein ...Cytoplasmic dynein-1, a microtubule (MT)-based motor protein, requires dynactin and a coiled-coil adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The roles of MTs and dynein regulator lissencephaly-1 (LIS1) in DDA assembly have remained elusive. Here we use cryo-electron microscopy to determine the structural basis of MT- and LIS1-mediated DDA assembly. We show that an adaptor-independent dynein-dynactin complex spontaneously forms on MTs with an intrinsic 2:1 stoichiometry in a highly efficient manner, driven by parallel alignment of dynein tails upon MT binding. Adaptors can wedge into and exchange within the assembled MT-bound dynein-dynactin complex; these processes are enabled by relative rotations between dynein and dynactin and facilitated by the dynein light-intermediate chains that assist the adaptor 'search' mechanism. Although LIS1 is dispensable for efficient DD(A)-MT assembly, its presence expands the conformational landscape of DD(A) assemblies on MTs. Cryo-electron microscopy reveals that LIS1 bridges dynactin p150 and dynein in both the closed Phi-like and open prepowerstroke states, stabilizing low-MT-affinity intermediates that tether dynein molecules in proximity to MTs and prime them for subsequent DD(A) assembly through alternative pathways. These findings demonstrate the dynamic adaptability of the dynein transport machinery and the coordinated roles of MTs and LIS1 in DDA assembly.
History
DepositionOct 10, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73175.png

Downloads & links

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Map

FileDownload / File: emd_73175.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of motor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B-ICD and LIS1
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.6 Å/pix.
x 200 pix.
= 520.8 Å		2.6 Å/pix.
x 200 pix.
= 520.8 Å		2.6 Å/pix.
x 200 pix.
= 520.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.604 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.5241375 - 1.1009157
Average (Standard dev.)-0.0029502811 (±0.046124745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 520.80005 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73175_msk_1.map
Projections & Slices
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Additional map: Unsharpened map of motor domain of human dynein-1...

Fileemd_73175_additional_1.map
AnnotationUnsharpened map of motor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B-ICD and LIS1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of motor domain of human dynein-1...

Fileemd_73175_half_map_1.map
AnnotationHalf map of motor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B-ICD and LIS1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of motor domain of human dynein-1...

Fileemd_73175_half_map_2.map
AnnotationHalf map of motor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B-ICD and LIS1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Sample components

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Entire : Motor domain of human dynein-1 in pre-power stroke bound to dynac...

EntireName: Motor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B-ICD and LIS1
Components
  • Complex: Motor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B-ICD and LIS1
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
    • Protein or peptide: Platelet-activating factor acetylhydrolase IB subunit beta
    • Protein or peptide: Cytoplasmic dynein 1 intermediate chain 2
    • Protein or peptide: Dynactin subunit 1
    • Protein or peptide: Dynein light chain 1, cytoplasmic
    • Protein or peptide: Dynein light chain Tctex-type 1
    • Protein or peptide: Cytoplasmic dynein 1 light intermediate chain 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Motor domain of human dynein-1 in pre-power stroke bound to dynac...

SupramoleculeName: Motor domain of human dynein-1 in pre-power stroke bound to dynactin-p150glued-CC1B-ICD and LIS1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cytoplasmic dynein 1 heavy chain 1

MacromoleculeName: Cytoplasmic dynein 1 heavy chain 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 533.08325 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSEPGGGGGE DGSAGLEVSA VQNVADVSVL QKHLRKLVPL LLEDGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVG DEGEEEKEFI SYNINIDIHY GVKSNSLAFI KRTPVIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP F FKSYIRES ...String:
MSEPGGGGGE DGSAGLEVSA VQNVADVSVL QKHLRKLVPL LLEDGGEAPA ALEAALEEKS ALEQMRKFLS DPQVHTVLVE RSTLKEDVG DEGEEEKEFI SYNINIDIHY GVKSNSLAFI KRTPVIDADK PVSSQLRVLT LSEDSPYETL HSFISNAVAP F FKSYIRES GKADRDGDKM APSVEKKIAE LEMGLLHLQQ NIEIPEISLP IHPMITNVAK QCYERGEKPK VTDFGDKVED PT FLNQLQS GVNRWIREIQ KVTKLDRDPA SGTALQEISF WLNLERALYR IQEKRESPEV LLTLDILKHG KRFHATVSFD TDT GLKQAL ETVNDYNPLM KDFPLNDLLS ATELDKIRQA LVAIFTHLRK IRNTKYPIQR ALRLVEAISR DLSSQLLKVL GTRK LMHVA YEEFEKVMVA CFEVFQTWDD EYEKLQVLLR DIVKRKREEN LKMVWRINPA HRKLQARLDQ MRKFRRQHEQ LRAVI VRVL RPQVTAVAQQ NQGEVPEPQD MKVAEVLFDA ADANAIEEVN LAYENVKEVD GLDVSKEGTE AWEAAMKRYD ERIDRV ETR ITARLRDQLG TAKNANEMFR IFSRFNALFV RPHIRGAIRE YQTQLIQRVK DDIESLHDKF KVQYPQSQAC KMSHVRD LP PVSGSIIWAK QIDRQLTAYM KRVEDVLGKG WENHVEGQKL KQDGDSFRMK LNTQEIFDDW ARKVQQRNLG VSGRIFTI E STRVRGRTGN VLKLKVNFLP EIITLSKEVR NLKWLGFRVP LAIVNKAHQA NQLYPFAISL IESVRTYERT CEKVEERNT ISLLVAGLKK EVQALIAEGI ALVWESYKLD PYVQRLAETV FNFQEKVDDL LIIEEKIDLE VRSLETCMYD HKTFSEILNR VQKAVDDLN LHSYSNLPIW VNKLDMEIER ILGVRLQAGL RAWTQVLLGQ AEDKAEVDMD TDAPQVSHKP GGEPKIKNVV H ELRITNQV IYLNPPIEEC RYKLYQEMFA WKMVVLSLPR IQSQRYQVGV HYELTEEEKF YRNALTRMPD GPVALEESYS AV MGIVSEV EQYVKVWLQY QCLWDMQAEN IYNRLGEDLN KWQALLVQIR KARGTFDNAE TKKEFGPVVI DYGKVQSKVN LKY DSWHKE VLSKFGQMLG SNMTEFHSQI SKSRQELEQH SVDTASTSDA VTFITYVQSL KRKIKQFEKQ VELYRNGQRL LEKQ RFQFP PSWLYIDNIE GEWGAFNDIM RRKDSAIQQQ VANLQMKIVQ EDRAVESRTT DLLTDWEKTK PVTGNLRPEE ALQAL TIYE GKFGRLKDDR EKCAKAKEAL ELTDTGLLSG SEERVQVALE ELQDLKGVWS ELSKVWEQID QMKEQPWVSV QPRKLR QNL DALLNQLKSF PARLRQYASY EFVQRLLKGY MKINMLVIEL KSEALKDRHW KQLMKRLHVN WVVSELTLGQ IWDVDLQ KN EAIVKDVLLV AQGEMALEEF LKQIREVWNT YELDLVNYQN KCRLIRGWDD LFNKVKEHIN SVSAMKLSPY YKVFEEDA L SWEDKLNRIM ALFDVWIDVQ RRWVYLEGIF TGSADIKHLL PVETQRFQSI STEFLALMKK VSKSPLVMDV LNIQGVQRS LERLADLLGK IQKALGEYLE RERSSFPRFY FVGDEDLLEI IGNSKNVAKL QKHFKKMFAG VSSIILNEDN SVVLGISSRE GEEVMFKTP VSITEHPKIN EWLTLVEKEM RVTLAKLLAE SVTEVEIFGK ATSIDPNTYI TWIDKYQAQL VVLSAQIAWS E NVETALSS MGGGGDAAPL HSVLSNVEVT LNVLADSVLM EQPPLRRRKL EHLITELVHQ RDVTRSLIKS KIDNAKSFEW LS QMRFYFD PKQTDVLQQL SIQMANAKFN YGFEYLGVQD KLVQTPLTDR CYLTMTQALE ARLGGSPFGP AGTGKTESVK ALG HQLGRF VLVFNCDETF DFQAMGRIFV GLCQVGAWGC FDEFNRLEER MLSAVSQQVQ CIQEALREHS NPNYDKTSAP ITCE LLNKQ VKVSPDMAIF ITMNPGYAGR SNLPDNLKKL FRSLAMTKPD RQLIAQVMLY SQGFRTAEVL ANKIVPFFKL CDEQL SSQS HYDFGLRALK SVLVSAGNVK RERIQKIKRE KEERGEAVDE GEIAENLPEQ EILIQSVCET MVPKLVAEDI PLLFSL LSD VFPGVQYHRG EMTALREELK KVCQEMYLTY GDGEEVGGMW VEKVLQLYQI TQINHGLMMV GPSGSGKSMA WRVLLKA LE RLEGVEGVAH IIDPKAISKD HLYGTLDPNT REWTDGLFTH VLRKIIDSVR GELQKRQWIV FDGDVDPEWV ENLNSVLD D NKLLTLPNGE RLSLPPNVRI MFEVQDLKYA TLATVSRCGM VWFSEDVLST DMIFNNFLAR LRSIPLDEGE DEAQRRRKG KEDEGEEAAS PMLQIQRDAA TIMQPYFTSN GLVTKALEHA FQLEHIMDLT RLRCLGSLFS MLHQACRNVA QYNANHPDFP MQIEQLERY IQRYLVYAIL WSLSGDSRLK MRAELGEYIR RITTVPLPTA PNIPIIDYEV SISGEWSPWQ AKVPQIEVET H KVAAPDVV VPTLDTVRHE ALLYTWLAEH KPLVLCGPPG SGKTMTLFSA LRALPDMEVV GLNFSSATTP ELLLKTFDHY CE YRRTPNG VVLAPVQLGK WLVLFCDEIN LPDMDKYGTQ RVISFIRQMV EHGGFYRTSD QTWVKLERIQ FVGACNPPTD PGR KPLSHR FLRHVPVVYV DYPGPASLTQ IYGTFNRAML RLIPSLRTYA EPLTAAMVEF YTMSQERFTQ DTQPHYIYSP REMT RWVRG IFEALRPLET LPVEGLIRIW AHEALRLFQD RLVEDEERRW TDENIDTVAL KHFPNIDREK AMSRPILYSN WLSKD YIPV DQEELRDYVK ARLKVFYEEE LDVPLVLFNE VLDHVLRIDR IFRQPQGHLL LIGVSGAGKT TLSRFVAWMN GLSVYQ IKV HRKYTGEDFD EDLRTVLRRS GCKNEKIAFI MDESNVLDSG FLERMNTLLA NGEVPGLFEG DEYATLMTQC KEGAQKE GL MLDSHEELYK WFTSQVIRNL HVVFTMNPSS EGLKDRAATS PALFNRCVLN WFGDWSTEAL YQVGKEFTSK MDLEKPNY I VPDYMPVVYD KLPQPPSHRE AIVNSCVFVH QTLHQANARL AKRGGRTMAI TPRHYLDFIN HYANLFHEKR SELEEQQMH LNVGLRKIKE TVDQVEELRR DLRIKSQELE VKNAAANDKL KKMVKDQQEA EKKKVMSQEI QEQLHKQQEV IADKQMSVKE DLDKVEPAV IEAQNAVKSI KKQHLVEVRS MANPPAAVKL ALESICLLLG ESTTDWKQIR SIIMRENFIP TIVNFSAEEI S DAIREKMK KNYMSNPSYN YEIVNRASLA CGPMVKWAIA QLNYADMLKR VEPLRNELQK LEDDAKDNQQ KANEVEQMIR DL EASIARY KEEYAVLISE AQAIKADLAA VEAKVNRSTA LLKSLSAERE RWEKTSETFK NQMSTIAGDC LLSAAFIAYA GYF DQQMRQ NLFTTWSHHL QQANIQFRTD IARTEYLSNA DERLRWQASS LPADDLCTEN AIMLKRFNRY PLIIDPSGQA TEFI MNEYK DRKITRTSFL DDAFRKNLES ALRFGNPLLV QDVESYDPVL NPVLNREVRR TGGRVLITLG DQDIDLSPSF VIFLS TRDP TVEFPPDLCS RVTFVNFTVT RSSLQSQCLN EVLKAERPDV DEKRSDLLKL QGEFQLRLRQ LEKSLLQALN EVKGRI LDD DTIITTLENL KREAAEVTRK VEETDIVMQE VETVSQQYLP LSTACSSIYF TMESLKQIHF LYQYSLQFFL DIYHNVL YE NPNLKGVTDH TQRLSIITKD LFQVAFNRVA RGMLHQDHIT FAMLLARIKL KGTVGEPTYD AEFQHFLRGN EIVLSAGS T PRIQGLTVEQ AEAVVRLSCL PAFKDLIAKV QADEQFGIWL DSSSPEQTVP YLWSEETPAT PIGQAIHRLL LIQAFRPDR LLAMAHMFVS TNLGESFMSI MEQPLDLTHI VGTEVKPNTP VLMCSVPGYD ASGHVEDLAA EQNTQITSIA IGSAEGFNQA DKAINTAVK SGRWVMLKNV HLAPGWLMQL EKKLHSLQPH ACFRLFLTME INPKVPVNLL RAGRIFVFEP PPGVKANMLR T FSSIPVSR ICKSPNERAR LYFLLAWFHA IIQERLRYAP LGWSKKYEFG ESDLRSACDT VDTWLDDTAK GRQNISPDKI PW SALKTLM AQSIYGGRVD NEFDQRLLNT FLERLFTTRS FDSEFKLACK VDGHKDIQMP DGIRREEFVQ WVELLPDTQT PSW LGLPNN AERVLLTTQG VDMISKMLKM QMLEDEDDLA YAETEKKTRT DSTSDGRPAW MRTLHTTASN WLHLIPQTLS HLKR TVENI KDPLFRFFER EVKMGAKLLQ DVRQDLADVV QVCEGKKKQT NYLRTLINEL VKGILPRSWS HYTVPAGMTV IQWVS DFSE RIKQLQNISL AAASGGAKEL KNIHVCLGGL FVPEAYITAT RQYVAQANSW SLEELCLEVN VTTSQGATLD ACSFGV TGL KLQGATCNNN KLSLSNAIST ALPLTQLRWV KQTNTEKKAS VVTLPVYLNF TRADLIFTVD FEIATKEDPR SFYERGV AV LCTE

UniProtKB: Cytoplasmic dynein 1 heavy chain 1

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Macromolecule #2: Platelet-activating factor acetylhydrolase IB subunit beta

MacromoleculeName: Platelet-activating factor acetylhydrolase IB subunit beta
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.709984 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVLSQRQRDE LNRAIADYLR SNGYEEAYSV FKKEAELDVN EELDKKYAGL LEKKWTSVIR LQKKVMELES KLNEAKEEFT SGGPLGQKR DPKEWIPRPP EKYALSGHRS PVTRVIFHPV FSVMVSASED ATIKVWDYET GDFERTLKGH TDSVQDISFD H SGKLLASC ...String:
MVLSQRQRDE LNRAIADYLR SNGYEEAYSV FKKEAELDVN EELDKKYAGL LEKKWTSVIR LQKKVMELES KLNEAKEEFT SGGPLGQKR DPKEWIPRPP EKYALSGHRS PVTRVIFHPV FSVMVSASED ATIKVWDYET GDFERTLKGH TDSVQDISFD H SGKLLASC SADMTIKLWD FQGFECIRTM HGHDHNVSSV AIMPNGDHIV SASRDKTIKM WEVQTGYCVK TFTGHREWVR MV RPNQDGT LIASCSNDQT VRVWVVATKE CKAELREHEH VVECISWAPE SSYSSISEAT GSETKKSGKP GPFLLSGSRD KTI KMWDVS TGMCLMTLVG HDNWVRGVLF HSGGKFILSC ADDKTLRVWD YKNKRCMKTL NAHEHFVTSL DFHKTAPYVV TGSV DQTVK VWECR

UniProtKB: Platelet-activating factor acetylhydrolase IB subunit beta

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Macromolecule #3: Cytoplasmic dynein 1 intermediate chain 2

MacromoleculeName: Cytoplasmic dynein 1 intermediate chain 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.546445 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSDKSELKAE LERKKQRLAQ IREEKKRKEE ERKKKETDQK KEAVAPVQEE SDLEKKRREA EALLQSMGLT PESPIVFSEY WVPPPMSPS SKSVSTPSEA GSQDSGDGAV GSRTLHWDTD PSVLQLHSDS DLGRGPIKLG MAKITQVDFP PREIVTYTKE T QTPVMAQP ...String:
MSDKSELKAE LERKKQRLAQ IREEKKRKEE ERKKKETDQK KEAVAPVQEE SDLEKKRREA EALLQSMGLT PESPIVFSEY WVPPPMSPS SKSVSTPSEA GSQDSGDGAV GSRTLHWDTD PSVLQLHSDS DLGRGPIKLG MAKITQVDFP PREIVTYTKE T QTPVMAQP KEDEEEDDDV VAPKPPIEPE EEKTLKKDEE NDSKAPPHEL TEEEKQQILH SEEFLSFFDH STRIVERALS EQ INIFFDY SGRDLEDKEG EIQAGAKLSL NRQFFDERWS KHRVVSCLDW SSQYPELLVA SYNNNEDAPH EPDGVALVWN MKY KKTTPE YVFHCQSAVM SATFAKFHPN LVVGGTYSGQ IVLWDNRSNK RTPVQRTPLS AAAHTHPVYC VNVVGTQNAH NLIS ISTDG KICSWSLDML SHPQDSMELV HKQSKAVAVT SMSFPVGDVN NFVVGSEEGS VYTACRHGSK AGISEMFEGH QGPIT GIHC HAAVGAVDFS HLFVTSSFDW TVKLWTTKNN KPLYSFEDNA DYVYDVMWSP THPALFACVD GMGRLDLWNL NNDTEV PTA SISVEGNPAL NRVRWTHSGR EIAVGDSEGQ IVIYDVGEQI AVPRNDEWAR FGRTLAEINA NRADAEEEAA TRIPA

UniProtKB: Cytoplasmic dynein 1 intermediate chain 2

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Macromolecule #4: Dynactin subunit 1

MacromoleculeName: Dynactin subunit 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 142.015484 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAQSKRHVYS RTPSGSRMSA EASARPLRVG SRVEVIGKGH RGTVAYVGAT LFATGKWVGV ILDEAKGKND GTVQGRKYFT CDEGHGIFV RQSQIQVFED GADTTSPETP DSSASKVLRR EGTDSNAKTS KLRGPKPKKA PTARKTTTRR PKPTRPASTG V AGASSSLG ...String:
MAQSKRHVYS RTPSGSRMSA EASARPLRVG SRVEVIGKGH RGTVAYVGAT LFATGKWVGV ILDEAKGKND GTVQGRKYFT CDEGHGIFV RQSQIQVFED GADTTSPETP DSSASKVLRR EGTDSNAKTS KLRGPKPKKA PTARKTTTRR PKPTRPASTG V AGASSSLG PSGSASAGEL SSSEPSTPAQ TPLAAPIIPT PALTSPGAAP PLPSPSKEEE GLRAQVRDLE EKLETLRLKR AE DKAKLKE LEKHKIQLEQ VQEWKSKMQE QQADLQRRLK EARKEAKEAL EAKERYMEEM ADTADAIEMA TLDKEMAEER AES LQQEVE ALKERVDELT TDLEILKAEI EEKGSDGAAS SYQLKQLEEQ NARLKDALVR MRDLSSSEKQ EHVKLQKLME KKNQ ELEVV RQQRERLQEE LSQAESTIDE LKEQVDAALG AEEMVEMLTD RNLNLEEKVR ELRETVGDLE AMNEMNDELQ ENARE TELE LREQLDMAGA RVREAQKRVE AAQETVADYQ QTIKKYRQLT AHLQDVNREL TNQQEASVER QQQPPPETFD FKIKFA ETK AHAKAIEMEL RQMEVAQANR HMSLLTAFMP DSFLRPGGDH DCVLVLLLMP RLICKAELIR KQAQEKFDLS ENCSERP GL RGAAGEQLSF AAGLVYSLSL LQATLHRYEH ALSQCSVDVY KKVGSLYPEM SAHERSLDFL IELLHKDQLD ETVNVEPL T KAIKYYQHLY SIHLAEQPED STMQLADHIK FTQSALDCMS VEVGRLRAFL QGGQEASDIA LLLRDLETSC SDIRQFCKK IRRRMPGTDA PGIPAALAFG AQVSDTLLDC RKHLTWVVAV LQEVAAAAAQ LIAPLAENEG LPVAALEELA FKASEQIYGT PSSSPYECL RQSCNILIST MNKLATAMQE GEYDAERPPS KPPPVELRAA ALRAEITDAE GLGLKLEDRE TVIKELKKSL K IKGEELSE ANVRLSLLEK KLDSAAKDAD ERIEKVQTRL EETQALLRKK EKEFEETMDA LQADIDQLEA EKAELKQRLN SQ SKRTIEG IRGPPPSGIA TLVSGIAGEE QQRGGAPGQA PGIVPGPGLV KDSPLLLQQI SAMRLHISQL QHENSVLKGA QMK ASLAAL PPLHVAKLSL PPHEGPGSEL AAGALYRKTN QLLETLNQLS THTHVVDITR SSPAAKSPSA QLLEQVTQLK SLSD TIEKL KDEVLKETVS QRPGATVPTD FATFPSSAFL RAKEEQQDDT VYMGKVTFSC AAGLGQRHRL VLTQEQLHQL HDRLI S

UniProtKB: Dynactin subunit 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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Macromolecule #6: Dynein light chain Tctex-type 1

MacromoleculeName: Dynein light chain Tctex-type 1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.461996 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MEDYQAAEET AFVVDEVSNI VKEAIESAIG GNAYQHSKVN QWTTNVVEQT LSQLTKLGKP FKYIVTCVIM QKNGAGLHTA SSCFWDSST DGSCTVRWEN KTMYCIVSAF GLSI

UniProtKB: Dynein light chain Tctex-type 1

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Macromolecule #7: Cytoplasmic dynein 1 light intermediate chain 2

MacromoleculeName: Cytoplasmic dynein 1 light intermediate chain 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.173156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAPVGVEKKL LLGPNGPAVA AAGDLTSEEE EGQSLWSSIL SEVSTRARSK LPSGKNILVF GEDGSGKTTL MTKLQGAEHG KKGRGLEYL YLSVHDEDRD DHTRCNVWIL DGDLYHKGLL KFAVSAESLP ETLVIFVADM SRPWTVMESL QKWASVLREH I DKMKIPPE ...String:
MAPVGVEKKL LLGPNGPAVA AAGDLTSEEE EGQSLWSSIL SEVSTRARSK LPSGKNILVF GEDGSGKTTL MTKLQGAEHG KKGRGLEYL YLSVHDEDRD DHTRCNVWIL DGDLYHKGLL KFAVSAESLP ETLVIFVADM SRPWTVMESL QKWASVLREH I DKMKIPPE KMRELERKFV KDFQDYMEPE EGCQGSPQRR GPLTSGSDEE NVALPLGDNV LTHNLGIPVL VVCTKCDAVS VL EKEHDYR DEHLDFIQSH LRRFCLQYGA ALIYTSVKEE KNLDLLYKYI VHKTYGFHFT TPALVVEKDA VFIPAGWDNE KKI AILHEN FTTVKPEDAY EDFIVKPPVR KLVHDKELAA EDEQVFLMKQ QSLLAKQPAT PTRASESPAR GPSGSPRTQG RGGP ASVPS SSPGTSVKKP DPNIKNNAAS EGVLASFFNS LLSKKTGSPG SPGAGGVQST AKKSGQKTVL SNVQEELDRM TRKPD SMVT NSSTENEA

UniProtKB: Cytoplasmic dynein 1 light intermediate chain 2

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Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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

Concentration2 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated defocus max: 2.6 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 45000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 52203
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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