9E0W: Human cytoplasmic dynein-1

Cryo-EM structure of human cytoplasmic dynein-1 bound to LIS1 in the presence of ATP. Determined by electron microscopy at 3.2 Å resolution. Released 9 Jul 2025.

Method
Electron microscopy
Resolution
3.2 Å
Organism
Homo sapiens
Chains
2
Atoms
24,531
Mol. weight
602.69 kDa
Ligands
MG, ATP, ADP
Released
9 Jul 2025

Explore 9E0W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E0W contains 134 α-helices and 97 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 132 helices, 67 β-strands

ElementResiduesLengthSheet
α-helix1557-15604
α-helix1562-158423
α-helix1588-15925
α-helix1597-161418
α-helix1618-16258
α-helix1627-16315
α-helix1634-16429
α-helix1650-16523
α-helix1654-16574
β-strand1663-166531
β-strand1672-167761
β-strand1683-169191
α-helix1698-172730
α-helix1735-174410
α-helix1747-176721
α-helix1776-179621
α-helix1802-182726
α-helix1836-18394
β-strand1843-184642
β-strand1857-186152
β-strand1864-186742
α-helix1878-18803
α-helix1883-189715
β-strand1901-190553
α-helix1913-192210
β-strand1927-192823
β-strand193113
α-helix1938-195114
β-strand1954-195853
α-helix1965-198521
β-strand1998-200144
β-strand2004-200744
β-strand2013-201863
α-helix2030-20334
β-strand2036-204053
α-helix2046-205712
α-helix2062-207918
α-helix2090-211324
α-helix2133-214513
α-helix2153-216412
α-helix2176-218813
α-helix2201-221616
β-strand2219-222355
α-helix2232-224514
β-strand2249-225465
α-helix2261-22655
β-strand226816
β-strand227516
α-helix2279-228911
β-strand2298-230365
α-helix2312-23154
β-strand2324-232637
β-strand2332-233437
β-strand2339-234355
α-helix2353-23564
β-strand2360-236345
α-helix2371-238313
α-helix2411-242313
α-helix2424-24263
α-helix2433-244210
α-helix2451-247525
α-helix2483-250220
α-helix2508-252114
α-helix2534-25363
β-strand2537-253938
β-strand2545-254738
α-helix2548-25514
α-helix2572-258514
β-strand2591-259449
α-helix2601-26099
β-strand2615-262069
α-helix2629-263810
β-strand2639-2644610
β-strand2647-2652610
β-strand2658-266369
α-helix2670-26723
α-helix2678-268811
β-strand2691-2694410
β-strand2699-2703510
β-strand2706-271279
α-helix2722-27243
α-helix2725-27284
β-strand2733-273539
α-helix2741-275515
α-helix2760-27656
α-helix2766-278116
α-helix2796-280914
α-helix2818-283316
α-helix2840-285718
α-helix2863-28664
β-strand2873-2874211
β-strand2882-2883211
α-helix2886-290116
α-helix2913-292715
β-strand2932-2936512
α-helix2943-295311
β-strand2957-2959312
α-helix2969-298416
β-strand2990-2995612
α-helix2996-29983
α-helix3002-301413
α-helix3024-304017
α-helix3048-306114
β-strand3062-3068712
α-helix3074-30818
α-helix3084-30874
β-strand3089-3093512
α-helix3097-30982
α-helix3099-310911
α-helix3121-31233
α-helix3139-316426
α-helix3173-323967
α-helix3451-349949
α-helix3503-351614
α-helix3522-353817
α-helix3549-35535
α-helix3556-35649
α-helix3571-358111
α-helix35861
β-strand3587-3590413
α-helix3595-36039
β-strand3610-3613413
α-helix3617-36193
α-helix3620-362910
β-strand3633-3636413
α-helix3638-36403
α-helix3643-36453
α-helix3646-36494
β-strand3654-3656314
β-strand3659-3664614
β-strand3667-3670414
α-helix3671-36722
β-strand3677-3681513
α-helix3690-36956
β-strand3697-3700413
α-helix3705-372016
α-helix3722-375433
α-helix3760-37623
α-helix3765-381753
α-helix3819-38224
α-helix3829-383911
α-helix3852-387221
α-helix3880-389415
α-helix3902-39098
α-helix3929-393810
α-helix3947-39537
α-helix3982-399615
α-helix3998-40003
α-helix4001-401313
α-helix4019-40224
α-helix4024-40252
α-helix4027-40293
α-helix4030-40345
β-strand4041-4045515
α-helix4052-406211
β-strand4066-4070515
α-helix4074-409017
β-strand4093-4097515
α-helix4099-41013
α-helix4103-411412
β-strand4124-4129615
α-helix4136-41416
β-strand4143-4147515
α-helix4149-41502
α-helix4153-416311
α-helix4166-41694
α-helix4176-419217
α-helix4209-422618
α-helix4240-42467
α-helix4247-42515
α-helix4259-427214
α-helix4275-42784
β-strand4283-4288616
β-strand4292-4295416
α-helix4302-43109
α-helix4318-43214
α-helix4329-434820
α-helix4380-439011
α-helix4391-43944
α-helix4408-443831
α-helix4446-445712
α-helix4460-44612
α-helix4475-449622
β-strand4508-4510317
α-helix4511-45133
α-helix4517-453216
α-helix4536-45383
β-strand4540-4544517
β-strand4558-4561417
β-strand4564-4566318
β-strand4568-4570318
β-strand4574-4577418
β-strand4584118
β-strand4588-4593617
β-strand4604-4610718
β-strand4618-4626918
α-helix46271
α-helix4632-46376
β-strand4641-4643318
Chain C: 2 helices, 30 β-strands
ElementResiduesLengthSheet
α-helix91-933
β-strand96119
β-strand102-105420
β-strand111-116621
β-strand123-127521
β-strand132-135421
β-strand144-146321
β-strand156-158322
β-strand164-168522
β-strand173-178622
β-strand184-189622
β-strand197-200423
β-strand206-210523
β-strand215-220623
β-strand226-231623
β-strand239-242424
β-strand249-252424
β-strand257-261524
β-strand268-273624
β-strand279-284625
α-helix287-29610
β-strand310-315625
β-strand319-324625
β-strand330-335625
β-strand341-346626
β-strand353-357526
β-strand361-366626
β-strand371-377726
β-strand383-388620
β-strand394-399620
β-strand403-408620
β-strand409119

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cytoplasmic dynein 1 heavy chain 1Aprotein4843Homo sapiensQ14204
Platelet-activating factor acetylhydrolase IB subunit betaCprotein411Homo sapiensP43034 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9E0W_1 Cytoplasmic dynein 1 heavy chain 1 (chains A)
GDYDIPTTENLYFQGDKDCEMKRTTLDSPLGKLELSGCEQGLHRIIFLGKGTSAADAVEV
PAPAAVLGGPEPLMQATAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVV
KFGEVISYSHLAALAGNPAATAAVKTALSGNPVPILIPCHRVVQGDLDVGGYEGGLAVKE
WLLAHEGHRLGKPGLGGSSEPGGGGGEDGSAGLEVSAVQNVADVSVLQKHLRKLVPLLLE
DGGEAPAALEAALEEKSALEQMRKFLSDPQVHTVLVERSTLKEDVGDEGEEEKEFISYNI
NIDIHYGVKSNSLAFIKRTPVIDADKPVSSQLRVLTLSEDSPYETLHSFISNAVAPFFKS
YIRESGKADRDGDKMAPSVEKKIAELEMGLLHLQQNIEIPEISLPIHPMITNVAKQCYER
GEKPKVTDFGDKVEDPTFLNQLQSGVNRWIREIQKVTKLDRDPASGTALQEISFWLNLER
ALYRIQEKRESPEVLLTLDILKHGKRFHATVSFDTDTGLKQALETVNDYNPLMKDFPLND
LLSATELDKIRQALVAIFTHLRKIRNTKYPIQRALRLVEAISRDLSSQLLKVLGTRKLMH
VAYEEFEKVMVACFEVFQTWDDEYEKLQVLLRDIVKRKREENLKMVWRINPAHRKLQARL
DQMRKFRRQHEQLRAVIVRVLRPQVTAVAQQNQGEVPEPQDMKVAEVLFDAADANAIEEV
NLAYENVKEVDGLDVSKEGTEAWEAAMKRYDERIDRVETRITARLRDQLGTAKNANEMFR
IFSRFNALFVRPHIRGAIREYQTQLIQRVKDDIESLHDKFKVQYPQSQACKMSHVRDLPP
VSGSIIWAKQIDRQLTAYMKRVEDVLGKGWENHVEGQKLKQDGDSFRMKLNTQEIFDDWA
RKVQQRNLGVSGRIFTIESTRVRGRTGNVLKLKVNFLPEIITLSKEVRNLKWLGFRVPLA
IVNKAHQANQLYPFAISLIESVRTYERTCEKVEERNTISLLVAGLKKEVQALIAEGIALV
WESYKLDPYVQRLAETVFNFQEKVDDLLIIEEKIDLEVRSLETCMYDHKTFSEILNRVQK
AVDDLNLHSYSNLPIWVNKLDMEIERILGVRLQAGLRAWTQVLLGQAEDKAEVDMDTDAP
QVSHKPGGEPKIKNVVHELRITNQVIYLNPPIEECRYKLYQEMFAWKMVVLSLPRIQSQR
YQVGVHYELTEEEKFYRNALTRMPDGPVALEESYSAVMGIVSEVEQYVKVWLQYQCLWDM
QAENIYNRLGEDLNKWQALLVQIRKARGTFDNAETKKEFGPVVIDYGKVQSKVNLKYDSW
HKEVLSKFGQMLGSNMTEFHSQISKSRQELEQHSVDTASTSDAVTFITYVQSLKRKIKQF
EKQVELYRNGQRLLEKQRFQFPPSWLYIDNIEGEWGAFNDIMRRKDSAIQQQVANLQMKI
VQEDRAVESRTTDLLTDWEKTKPVTGNLRPEEALQALTIYEGKFGRLKDDREKCAKAKEA
LELTDTGLLSGSEERVQVALEELQDLKGVWSELSKVWEQIDQMKEQPWVSVQPRKLRQNL
DALLNQLKSFPARLRQYASYEFVQRLLKGYMKINMLVIELKSEALKDRHWKQLMKRLHVN
WVVSELTLGQIWDVDLQKNEAIVKDVLLVAQGEMALEEFLKQIREVWNTYELDLVNYQNK
CRLIRGWDDLFNKVKEHINSVSAMKLSPYYKVFEEDALSWEDKLNRIMALFDVWIDVQRR
WVYLEGIFTGSADIKHLLPVETQRFQSISTEFLALMKKVSKSPLVMDVLNIQGVQRSLER
LADLLGKIQKALGEYLERERSSFPRFYFVGDEDLLEIIGNSKNVAKLQKHFKKMFAGVSS
IILNEDNSVVLGISSREGEEVMFKTPVSITEHPKINEWLTLVEKEMRVTLAKLLAESVTE
VEIFGKATSIDPNTYITWIDKYQAQLVVLSAQIAWSENVETALSSMGGGGDAAPLHSVLS
NVEVTLNVLADSVLMEQPPLRRRKLEHLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMR
FYFDPKQTDVLQQLSIQMANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEARLGGS
PFGPAGTGKTESVKALGHQLGRFVLVFNCDETFDFQAMGRIFVGLCQVGAWGCFDEFNRL
EERMLSAVSQQVQCIQEALREHSNPNYDKTSAPITCELLNKQVKVSPDMAIFITMNPGYA
GRSNLPDNLKKLFRSLAMTKPDRQLIAQVMLYSQGFRTAEVLANKIVPFFKLCDEQLSSQ
SHYDFGLRALKSVLVSAGNVKRERIQKIKREKEERGEAVDEGEIAENLPEQEILIQSVCE
TMVPKLVAEDIPLLFSLLSDVFPGVQYHRGEMTALREELKKVCQEMYLTYGDGEEVGGMW
VEKVLQLYQITQINHGLMMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAISKDH
LYGTLDPNTREWTDGLFTHVLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSVLDDNK
LLTLPNGERLSLPPNVRIMFEVQDLKYATLATVSRCGMVWFSEDVLSTDMIFNNFLARLR
SIPLDEGEDEAQRRRKGKEDEGEEAASPMLQIQRDAATIMQPYFTSNGLVTKALEHAFQL
EHIMDLTRLRCLGSLFSMLHQACRNVAQYNANHPDFPMQIEQLERYIQRYLVYAILWSLS
GDSRLKMRAELGEYIRRITTVPLPTAPNIPIIDYEVSISGEWSPWQAKVPQIEVETHKVA
APDVVVPTLDTVRHEALLYTWLAEHKPLVLCGPPGSGKTMTLFSALRALPDMEVVGLNFS
SATTPELLLKTFDHYCEYRRTPNGVVLAPVQLGKWLVLFCDEINLPDMDKYGTQRVISFI
RQMVEHGGFYRTSDQTWVKLERIQFVGACNPPTDPGRKPLSHRFLRHVPVVYVDYPGPAS
LTQIYGTFNRAMLRLIPSLRTYAEPLTAAMVEFYTMSQERFTQDTQPHYIYSPREMTRWV
RGIFEALRPLETLPVEGLIRIWAHEALRLFQDRLVEDEERRWTDENIDTVALKHFPNIDR
EKAMSRPILYSNWLSKDYIPVDQEELRDYVKARLKVFYEEELDVPLVLFNEVLDHVLRID
RIFRQPQGHLLLIGVSGAGKTTLSRFVAWMNGLSVYQIKVHRKYTGEDFDEDLRTVLRRS
GCKNEKIAFIMDESNVLDSGFLERMNTLLANGEVPGLFEGDEYATLMTQCKEGAQKEGLM
LDSHEELYKWFTSQVIRNLHVVFTMNPSSEGLKDRAATSPALFNRCVLNWFGDWSTEALY
QVGKEFTSKMDLEKPNYIVPDYMPVVYDKLPQPPSHREAIVNSCVFVHQTLHQANARLAK
RGGRTMAITPRHYLDFINHYANLFHEKRSELEEQQMHLNVGLRKIKETVDQVEELRRDLR
IKSQELEVKNAAANDKLKKMVKDQQEAEKKKVMSQEIQEQLHKQQEVIADKQMSVKEDLD
KVEPAVIEAQNAVKSIKKQHLVEVRSMANPPAAVKLALESICLLLGESTTDWKQIRSIIM
RENFIPTIVNFSAEEISDAIREKMKKNYMSNPSYNYEIVNRASLACGPMVKWAIAQLNYA
DMLKRVEPLRNELQKLEDDAKDNQQKANEVEQMIRDLEASIARYKEEYAVLISEAQAIKA
DLAAVEAKVNRSTALLKSLSAERERWEKTSETFKNQMSTIAGDCLLSAAFIAYAGYFDQQ
MRQNLFTTWSHHLQQANIQFRTDIARTEYLSNADERLRWQASSLPADDLCTENAIMLKRF
NRYPLIIDPSGQATEFIMNEYKDRKITRTSFLDDAFRKNLESALRFGNPLLVQDVESYDP
VLNPVLNREVRRTGGRVLITLGDQDIDLSPSFVIFLSTRDPTVEFPPDLCSRVTFVNFTV
TRSSLQSQCLNEVLKAERPDVDEKRSDLLKLQGEFQLRLRQLEKSLLQALNEVKGRILDD
DTIITTLENLKREAAEVTRKVEETDIVMQEVETVSQQYLPLSTACSSIYFTMESLKQIHF
LYQYSLQFFLDIYHNVLYENPNLKGVTDHTQRLSIITKDLFQVAFNRVARGMLHQDHITF
AMLLARIKLKGTVGEPTYDAEFQHFLRGNEIVLSAGSTPRIQGLTVEQAEAVVRLSCLPA
FKDLIAKVQADEQFGIWLDSSSPEQTVPYLWSEETPATPIGQAIHRLLLIQAFRPDRLLA
MAHMFVSTNLGESFMSIMEQPLDLTHIVGTEVKPNTPVLMCSVPGYDASGHVEDLAAEQN
TQITSIAIGSAEGFNQADKAINTAVKSGRWVMLKNVHLAPGWLMQLEKKLHSLQPHACFR
LFLTMEINPKVPVNLLRAGRIFVFEPPPGVKANMLRTFSSIPVSRICKSPNERARLYFLL
AWFHAIIQERLRYAPLGWSKKYEFGESDLRSACDTVDTWLDDTAKGRQNISPDKIPWSAL
KTLMAQSIYGGRVDNEFDQRLLNTFLERLFTTRSFDSEFKLACKVDGHKDIQMPDGIRRE
EFVQWVELLPDTQTPSWLGLPNNAERVLLTTQGVDMISKMLKMQMLEDEDDLAYAETEKK
TRTDSTSDGRPAWMRTLHTTASNWLHLIPQTLSHLKRTVENIKDPLFRFFEREVKMGAKL
LQDVRQDLADVVQVCEGKKKQTNYLRTLINELVKGILPRSWSHYTVPAGMTVIQWVSDFS
ERIKQLQNISLAAASGGAKELKNIHVCLGGLFVPEAYITATRQYVAQANSWSLEELCLEV
NVTTSQGATLDACSFGVTGLKLQGATCNNNKLSLSNAISTALPLTQLRWVKQTNTEKKAS
VVTLPVYLNFTRADLIFTVDFEIATKEDPRSFYERGVAVLCTE
Sequence of entity 2 (C), FASTA
>9E0W_2 Platelet-activating factor acetylhydrolase IB subunit beta (chains C)
GSVLSQRQRDELNRAIADYLRSNGYEEAYSVFKKEAELDVNEELDKKYAGLLEKKWTSVI
RLQKKVMELESKLNEAKEEFTSGGPLGQKRDPKEWIPRPPEKYALSGHRSPVTRVIFHPV
FSVMVSASEDATIKVWDYETGDFERTLKGHTDSVQDISFDHSGKLLASCSADMTIKLWDF
QGFECIRTMHGHDHNVSSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRM
VRPNQDGTLIASCSNDQTVRVWVVATKECKAELREHEHVVECISWAPESSYSSISEATGS
ETKKSGKPGPFLLSGSRDKTIKMWDVSTGMCLMTLVGHDNWVRGVLFHSGGKFILSCADD
KTLRVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGSVDQTVKVWECR

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg2
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P23

Primary citation

Cryo-EM captures early intermediate steps in dynein activation by LIS1. Nguyen, K.H.V., Karasmanis, E.P., Kendrick, A.A. et al. Nat Commun (2025) 16:7054-7054. DOI 10.1038/s41467-025-62185-z · PubMed

Other PDB entries of the same protein (UniProt Q14204), best resolution first:

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