9E0T: 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 3.1 Å resolution. Released 9 Jul 2025.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 27,918
Mol. weight: 649.41 kDa
Ligands: ATP, MG, ADP
Released: 9 Jul 2025

Explore 9E0T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E0T contains 138 α-helices and 137 β-strands across 3 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: 134 helices, 74 β-strands

Element	Residues	Length	Sheet
α-helix	1445-1471	27
β-strand	1474	1	1
β-strand	1477-1480	4	2
β-strand	1484-1487	4	2
α-helix	1490-1509	20
α-helix	1513-1515	3
α-helix	1517-1553	37
α-helix	1562-1584	23
β-strand	1587	1	1
α-helix	1588-1592	5
α-helix	1597-1614	18
α-helix	1617-1623	7
α-helix	1627-1631	5
α-helix	1634-1642	9
α-helix	1648-1652	5
α-helix	1654-1657	4
β-strand	1663-1666	4	3
β-strand	1672-1677	6	3
β-strand	1683-1691	9	3
α-helix	1698-1727	30
α-helix	1735-1744	10
α-helix	1747-1766	20
α-helix	1776-1796	21
α-helix	1802-1827	26
α-helix	1836-1840	5
β-strand	1843-1846	4	4
α-helix	1853-1855	3
β-strand	1857-1861	5	4
β-strand	1864-1867	4	4
α-helix	1878-1880	3
α-helix	1883-1897	15
β-strand	1901-1905	5	5
α-helix	1913-1922	10
β-strand	1927-1928	2	5
β-strand	1931	1	5
α-helix	1938-1951	14
β-strand	1954-1958	5	5
α-helix	1965-1986	22
β-strand	1998-2000	3	6
β-strand	2005-2007	3	6
β-strand	2013-2018	6	5
α-helix	2025-2029	5
α-helix	2030-2033	4
β-strand	2036-2040	5	5
α-helix	2046-2057	12
α-helix	2062-2079	18
α-helix	2090-2113	24
α-helix	2133-2145	13
α-helix	2154-2164	11
α-helix	2176-2188	13
α-helix	2201-2216	16
β-strand	2220-2223	4	7
α-helix	2230-2245	16
β-strand	2249-2254	6	8
α-helix	2261-2265	5
β-strand	2266-2268	3	9
β-strand	2275-2277	3	9
α-helix	2279-2289	11
β-strand	2298-2303	6	8
α-helix	2312-2315	4
α-helix	2316-2319	4
β-strand	2324-2326	3	10
β-strand	2332-2334	3	10
α-helix	2335-2336	2
β-strand	2339-2343	5	8
β-strand	2344-2345	2	7
α-helix	2353-2356	4
β-strand	2360-2363	4	7
α-helix	2371-2383	13
α-helix	2411-2427	17
α-helix	2433-2442	10
α-helix	2451-2475	25
α-helix	2483-2502	20
α-helix	2508-2521	14
α-helix	2534-2536	3
β-strand	2537-2539	3	11
β-strand	2545-2547	3	11
α-helix	2572-2586	15
β-strand	2591-2594	4	12
α-helix	2601-2610	10
β-strand	2615-2620	6	12
α-helix	2629-2638	10
β-strand	2639-2644	6	13
β-strand	2647-2652	6	13
α-helix	2657	1
β-strand	2658-2663	6	12
α-helix	2670-2672	3
α-helix	2678-2688	11
β-strand	2691-2694	4	13
β-strand	2699-2703	5	13
β-strand	2706-2712	7	12
α-helix	2722-2724	3
α-helix	2725-2728	4
β-strand	2733-2735	3	12
α-helix	2740-2755	16
α-helix	2763-2765	3
α-helix	2766-2783	18
α-helix	2796-2810	15
α-helix	2818-2833	16
α-helix	2840-2857	18
α-helix	2863-2866	4
β-strand	2873-2874	2	14
β-strand	2882-2883	2	14
α-helix	2886-2903	18
α-helix	2913-2927	15
β-strand	2933-2936	4	15
α-helix	2943-2953	11
β-strand	2957-2959	3	15
α-helix	2969-2984	16
β-strand	2990-2995	6	15
α-helix	2996-2998	3
α-helix	3002-3014	13
α-helix	3024-3040	17
α-helix	3048-3061	14
β-strand	3062-3068	7	15
α-helix	3072-3081	10
α-helix	3084-3087	4
β-strand	3090-3093	4	15
α-helix	3097-3098	2
α-helix	3099-3109	11
α-helix	3139-3164	26
α-helix	3173-3239	67
α-helix	3452-3499	48
α-helix	3503-3516	14
α-helix	3522-3538	17
α-helix	3556-3564	9
α-helix	3571-3581	11
α-helix	3586	1
β-strand	3587-3590	4	16
α-helix	3595-3603	9
β-strand	3610-3613	4	16
α-helix	3617-3619	3
α-helix	3620-3629	10
β-strand	3633-3636	4	16
α-helix	3643-3645	3
α-helix	3646-3650	5
β-strand	3654-3656	3	17
β-strand	3659-3664	6	17
β-strand	3667-3670	4	17
β-strand	3677-3681	5	16
α-helix	3690-3695	6
β-strand	3697-3700	4	16
α-helix	3705-3720	16
α-helix	3722-3754	33
α-helix	3760-3762	3
α-helix	3765-3817	53
α-helix	3818-3820	3
α-helix	3829-3839	11
α-helix	3852-3872	21
α-helix	3880-3893	14
α-helix	3902-3910	9
α-helix	3929-3938	10
α-helix	3947-3953	7
α-helix	3982-3996	15
α-helix	3998-4000	3
α-helix	4001-4013	13
α-helix	4019-4022	4
α-helix	4024-4025	2
α-helix	4027-4033	7
β-strand	4041-4045	5	18
α-helix	4052-4062	11
β-strand	4067-4070	4	18
α-helix	4074-4089	16
β-strand	4094-4097	4	18
α-helix	4099-4101	3
α-helix	4103-4114	12
β-strand	4124-4129	6	18
α-helix	4136-4141	6
β-strand	4143-4144	2	18
β-strand	4147	1	18
α-helix	4149-4150	2
α-helix	4153-4163	11
α-helix	4166-4169	4
α-helix	4176-4192	17
α-helix	4209-4226	18
α-helix	4235-4237	3
α-helix	4240-4246	7
α-helix	4247-4251	5
α-helix	4253-4255	3
α-helix	4259-4272	14
α-helix	4275-4278	4
β-strand	4283-4288	6	19
β-strand	4292-4295	4	19
α-helix	4296-4297	2
α-helix	4302-4310	9
α-helix	4325-4328	4
α-helix	4329-4347	19
α-helix	4380-4390	11
α-helix	4391-4394	4
α-helix	4408-4438	31
α-helix	4446-4457	12
α-helix	4459-4461	3
α-helix	4475-4497	23
β-strand	4508-4510	3	20
α-helix	4517-4532	16
α-helix	4536-4538	3
β-strand	4540-4544	5	20
β-strand	4558-4561	4	20
β-strand	4564-4565	2	21
β-strand	4568-4570	3	22
β-strand	4575-4577	3	22
β-strand	4584	1	21
β-strand	4588-4593	6	20
β-strand	4604-4610	7	21
β-strand	4618-4625	8	21
β-strand	4626	1	22
α-helix	4632-4637	6
β-strand	4642-4643	2	21

Chain B: 2 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	91-93	3
β-strand	96	1	23
β-strand	102-105	4	24
β-strand	111-116	6	25
β-strand	123-127	5	25
β-strand	132-136	5	25
β-strand	141-146	6	25
β-strand	153-157	5	26
β-strand	164-169	6	26
β-strand	174-178	5	26
β-strand	184-188	5	26
β-strand	195-199	5	27
β-strand	206-211	6	27
β-strand	215-220	6	27
β-strand	226-231	6	27
β-strand	237-242	6	28
β-strand	248-253	6	28
β-strand	260-262	3	28
β-strand	270	1	28
β-strand	279-284	6	29
α-helix	287-296	10
β-strand	310-315	6	29
β-strand	320-324	5	29
β-strand	330-334	5	29
β-strand	341-346	6	30
β-strand	353-357	5	30
β-strand	361-365	5	30
β-strand	374-377	4	30
β-strand	383-388	6	24
β-strand	394-399	6	24
β-strand	403-408	6	24
β-strand	409	1	23

Chain C: 2 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	91-93	3
β-strand	96	1	31
β-strand	102-105	4	32
β-strand	111-116	6	33
β-strand	123-127	5	33
β-strand	131-136	6	33
β-strand	141-147	7	33
β-strand	153-158	6	34
β-strand	164-169	6	34
β-strand	173-178	6	34
β-strand	184-188	5	34
β-strand	195-200	6	35
β-strand	206-211	6	35
β-strand	215-220	6	35
β-strand	225-231	7	35
β-strand	237-242	6	36
β-strand	248-253	6	36
β-strand	258-262	5	36
β-strand	268	1	36
β-strand	272	1	36
β-strand	279-284	6	37
α-helix	290-296	7
β-strand	310-315	6	37
β-strand	319-324	6	37
β-strand	329-335	7	37
β-strand	341-345	5	38
β-strand	353-357	5	38
β-strand	362-365	4	38
β-strand	372-376	5	38
β-strand	383	1	39
β-strand	387-388	2	32
β-strand	394-397	4	32
β-strand	399	1	39
β-strand	403-408	6	32
β-strand	409	1	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytoplasmic dynein 1 heavy chain 1	A	protein	4843	Homo sapiens	Q14204
Platelet-activating factor acetylhydrolase IB subunit beta	B, C	protein	411	Homo sapiens	P43034 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9E0T_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 (B, C), FASTA

>9E0T_2 Platelet-activating factor acetylhydrolase IB subunit beta (chains B, C)
GSVLSQRQRDELNRAIADYLRSNGYEEAYSVFKKEAELDVNEELDKKYAGLLEKKWTSVI
RLQKKVMELESKLNEAKEEFTSGGPLGQKRDPKEWIPRPPEKYALSGHRSPVTRVIFHPV
FSVMVSASEDATIKVWDYETGDFERTLKGHTDSVQDISFDHSGKLLASCSADMTIKLWDF
QGFECIRTMHGHDHNVSSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRM
VRPNQDGTLIASCSNDQTVRVWVVATKECKAELREHEHVVECISWAPESSYSSISEATGS
ETKKSGKPGPFLLSGSRDKTIKMWDVSTGMCLMTLVGHDNWVRGVLFHSGGKFILSCADD
KTLRVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGSVDQTVKVWECR

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
MG	Magnesium ion	Mg	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3

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:

5OWO 1.79 Å, Human cytoplasmic Dynein N-Terminus dimerization domain at 1.8 Angstrom resolution
9BLZ 2.2 Å, State-1(phi motor) of full-length human dynein-1 in 5mM ATP
9BMR 2.6 Å, State-1 of motor domain from full-length human phi dynein-1 in 5 mM ADP
9DH5 2.6 Å, State-1 of the motor domain from full-length human dynein-1 in 5mM AMPPNP with 5mM Mg2+
9E0X 2.7 Å, Cryo-EM structure of Phi dynein
9E10 2.71 Å, Dimeric motor domains from phi dynein-1 under Lis1 condition
9BM0 2.8 Å, State-2 of motor domain from full-length human dynein-1 in 5mM ATP
9BMF 2.8 Å, State-1(phi motor) of full-length human dynein-1 in 5mM ATPVi
9BMH 2.8 Å, State-4 of motor domain from full-length human dynein-1 in 5mM ATPVi
9BN3 2.8 Å, The alpha registry-locked dynein motor domain mutant in 5mM ATP condition, class1
9BM2 2.82 Å, State-4 of motor domain from full-length human dynein-1 in 5 mM ATP
9BMG 2.86 Å, State-2 of full-length human dynein-1 in 5mM ATPVi

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