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- EMDB-47382: Full-length human dynein-1 in phi-like comformation bound to a Li... -

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Basic information

Entry
Database: EMDB / ID: EMD-47382
TitleFull-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Lis1 condition
Map dataFull-length human dynein-1 in Phi-liker comformation bound to a Lis1 dimer under Lis1 condition
Sample
  • Complex: Full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Lis1 condition
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
    • Protein or peptide: Cytoplasmic dynein 1 intermediate chain 2
    • Protein or peptide: Cytoplasmic dynein 1 light intermediate chain 2
    • Protein or peptide: Dynein light chain roadblock-type 1
    • Protein or peptide: Dynein light chain 1, cytoplasmic
    • Protein or peptide: Dynein light chain Tctex-type 1
    • Protein or peptide: Platelet-activating factor acetylhydrolase IB subunit beta
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsdynein-1 / phi-like conformation / Lis1 / MOTOR PROTEIN
Function / homology
Function and homology information


intracellular transport of viral protein in host cell / nitric-oxide synthase inhibitor activity / microtubule cytoskeleton organization involved in establishment of planar polarity / establishment of planar polarity of embryonic epithelium / negative regulation of DNA strand resection involved in replication fork processing / 1-alkyl-2-acetylglycerophosphocholine esterase complex / cerebral cortex neuron differentiation / secretory vesicle / visual behavior / corpus callosum morphogenesis ...intracellular transport of viral protein in host cell / nitric-oxide synthase inhibitor activity / microtubule cytoskeleton organization involved in establishment of planar polarity / establishment of planar polarity of embryonic epithelium / negative regulation of DNA strand resection involved in replication fork processing / 1-alkyl-2-acetylglycerophosphocholine esterase complex / cerebral cortex neuron differentiation / secretory vesicle / visual behavior / corpus callosum morphogenesis / establishment of centrosome localization / platelet activating factor metabolic process / acrosome assembly / platelet activating factor catabolic process / layer formation in cerebral cortex / central region of growth cone / intraciliary retrograde transport / auditory receptor cell development / microtubule sliding / dynein light chain binding / transport along microtubule / dynein heavy chain binding / negative regulation of phosphorylation / Activation of BIM and translocation to mitochondria / motile cilium assembly / neuroblast proliferation / microtubule organizing center organization / positive regulation of embryonic development / brain morphogenesis / astral microtubule / cortical microtubule organization / reelin-mediated signaling pathway / Intraflagellar transport / positive regulation of dendritic spine morphogenesis / positive regulation of intracellular transport / positive regulation of spindle assembly / germ cell development / regulation of metaphase plate congression / stem cell division / neuromuscular process controlling balance / stereocilium / establishment of spindle localization / microtubule plus-end binding / regulation of G protein-coupled receptor signaling pathway / microtubule-dependent intracellular transport of viral material towards nucleus / positive regulation of mitotic cell cycle spindle assembly checkpoint / motile cilium / vesicle transport along microtubule / retrograde axonal transport / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / P-body assembly / microtubule associated complex / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / microtubule motor activity / kinesin complex / spermatid development / microtubule-based movement / male germ cell nucleus / Macroautophagy / establishment of mitotic spindle orientation / dynein intermediate chain binding / cell leading edge / transmission of nerve impulse / tertiary granule membrane / dynein complex binding / ciliary tip / cochlea development / dynactin binding / ficolin-1-rich granule membrane / positive regulation of axon extension / adult locomotory behavior / microtubule-based process / COPI-mediated anterograde transport / cytoplasmic microtubule / positive regulation of mitotic cell cycle / phospholipase binding / cytoplasmic microtubule organization / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / substantia nigra development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / AURKA Activation by TPX2 / hippocampus development / Resolution of Sister Chromatid Cohesion / stress granule assembly / enzyme inhibitor activity / mitotic spindle organization / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of mitotic spindle organization
Similarity search - Function
: / : / PAC1 LisH domain / Dynein 1 light intermediate chain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein light chain roadblock-type 1/2 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) ...: / : / PAC1 LisH domain / Dynein 1 light intermediate chain / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Dynein light chain roadblock-type 1/2 / 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 / : / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / 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 / Cytoplasmic dynein 1 heavy chain 1 / Dynein light chain roadblock-type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsYang J / 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: Nat Chem Biol / Year: 2026
Title: Nde1 promotes Lis1 binding to full-length autoinhibited human dynein 1.
Authors: Jun Yang / Yuanchang Zhao / Pengxin Chai / Ahmet Yildiz / Kai Zhang /
Abstract: Cytoplasmic dynein 1 (dynein) is the primary motor responsible for the retrograde transport of intracellular cargoes along microtubules. Activation of dynein requires the opening its autoinhibited ...Cytoplasmic dynein 1 (dynein) is the primary motor responsible for the retrograde transport of intracellular cargoes along microtubules. Activation of dynein requires the opening its autoinhibited Phi conformation, a process driven by Lis1 and Nde1/Ndel1. Using biochemical reconstitution and cryo-electron microscopy, we demonstrate that Nde1 enhances Lis1 binding to autoinhibited dynein and facilitates Phi opening. We identify a key intermediate in this activation pathway where a single Lis1 dimer binds between Phi-like (Phi) motor rings. In this 'Phi-Lis1' complex, Lis1 interacts with one motor domain through canonical sites at the AAA+ (adenosine triphosphatases associated with diverse cellular activities) ring and stalk, and with AAA5, AAA6 and linker regions of the other motor domain. Mutagenesis and motility assays confirm the critical role of the Phi-Lis1 interface in dynein activation. This intermediate forms rapidly in the presence of Nde1, although Nde1 is not part of Phi-Lis1. These findings provide key insights into how Nde1 promotes Lis1-mediated Phi opening.
History
DepositionOct 21, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47382.png

Downloads & links

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Map

FileDownload / File: emd_47382.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull-length human dynein-1 in Phi-liker comformation bound to a Lis1 dimer under Lis1 condition
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.74 Å/pix.
x 420 pix.
= 729.12 Å		1.74 Å/pix.
x 420 pix.
= 729.12 Å		1.74 Å/pix.
x 420 pix.
= 729.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.736 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum0.0 - 4.7432194
Average (Standard dev.)0.0021615431 (±0.017301325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 729.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Full-length human dynein-1 in phi-like comformation bound to a Li...

EntireName: Full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Lis1 condition
Components
  • Complex: Full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Lis1 condition
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
    • Protein or peptide: Cytoplasmic dynein 1 intermediate chain 2
    • Protein or peptide: Cytoplasmic dynein 1 light intermediate chain 2
    • Protein or peptide: Dynein light chain roadblock-type 1
    • Protein or peptide: Dynein light chain 1, cytoplasmic
    • Protein or peptide: Dynein light chain Tctex-type 1
    • Protein or peptide: Platelet-activating factor acetylhydrolase IB subunit beta
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Full-length human dynein-1 in phi-like comformation bound to a Li...

SupramoleculeName: Full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Lis1 condition
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.5 MDa

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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: 2 / 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: Cytoplasmic dynein 1 intermediate chain 2

MacromoleculeName: Cytoplasmic dynein 1 intermediate chain 2 / type: protein_or_peptide / ID: 2 / 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 #3: Cytoplasmic dynein 1 light intermediate chain 2

MacromoleculeName: Cytoplasmic dynein 1 light intermediate chain 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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 #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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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: Platelet-activating factor acetylhydrolase IB subunit beta

MacromoleculeName: Platelet-activating factor acetylhydrolase IB subunit beta
type: protein_or_peptide / ID: 7 / 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 #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 6 / 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: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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
Details: 25 mM HEPES pH 7.2, 150 mM KCl, 1 mM MgCl2, 5 mM DTT, 3 mM ATP
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 127963
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)

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