9E22: 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 3.3 Å resolution. Released 9 Jul 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 24,612
Mol. weight: 602.74 kDa
Ligands: MG, ATP, ADP
Released: 9 Jul 2025

Explore 9E22 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E22 contains 136 α-helices and 104 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: 135 helices, 77 β-strands

Element	Residues	Length	Sheet
α-helix	1450-1472	23
β-strand	1474	1	1
β-strand	1476-1480	5	2
β-strand	1484-1488	5	2
α-helix	1490-1507	18
α-helix	1517-1552	36
α-helix	1557-1560	4
α-helix	1562-1584	23
β-strand	1587	1	1
α-helix	1588-1592	5
α-helix	1597-1625	29
α-helix	1634-1642	9
α-helix	1650-1657	8
β-strand	1663-1666	4	3
β-strand	1672	1	4
β-strand	1673-1677	5	3
β-strand	1683-1685	3	3
α-helix	1689-1690	2
β-strand	1691	1	4
α-helix	1698-1729	32
α-helix	1735-1744	10
α-helix	1747-1769	23
α-helix	1776-1797	22
α-helix	1802-1828	27
α-helix	1836-1839	4
β-strand	1843-1846	4	5
β-strand	1857-1861	5	5
β-strand	1864-1867	4	5
α-helix	1877-1880	4
α-helix	1883-1897	15
β-strand	1901	1	6
β-strand	1902	1	7
β-strand	1904-1905	2	8
α-helix	1912-1922	11
β-strand	1927-1930	4	7
α-helix	1938-1951	14
β-strand	1954-1957	4	7
α-helix	1960-1962	3
α-helix	1965-1983	19
β-strand	1998-2001	4	9
β-strand	2004-2007	4	9
β-strand	2013-2016	4	7
β-strand	2018	1	8
β-strand	2036	1	6
β-strand	2039-2040	2	8
α-helix	2046-2056	11
α-helix	2063-2079	17
α-helix	2090-2117	28
α-helix	2124-2129	6
α-helix	2133-2145	13
α-helix	2153-2164	12
α-helix	2176-2188	13
α-helix	2201-2216	16
β-strand	2219	1	10
β-strand	2220-2222	3	11
α-helix	2230-2245	16
β-strand	2249-2254	6	10
α-helix	2261-2265	5
β-strand	2267-2268	2	12
β-strand	2275-2276	2	12
α-helix	2279-2289	11
β-strand	2298-2304	7	10
α-helix	2316-2319	4
β-strand	2324-2325	2	13
β-strand	2333-2334	2	13
β-strand	2339-2344	6	10
α-helix	2353-2357	5
β-strand	2360-2362	3	11
α-helix	2371-2384	14
α-helix	2395-2398	4
α-helix	2411-2423	13
α-helix	2432-2442	11
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	14
β-strand	2545-2547	3	14
α-helix	2548-2550	3
α-helix	2568-2569	2
α-helix	2572-2585	14
β-strand	2592-2594	3	15
α-helix	2601-2610	10
β-strand	2615-2618	4	16
α-helix	2628-2638	11
β-strand	2639-2643	5	17
β-strand	2648-2652	5	17
β-strand	2658-2663	6	16
α-helix	2670-2671	2
α-helix	2678-2689	12
β-strand	2693	1	18
β-strand	2700	1	18
β-strand	2701-2703	3	17
β-strand	2706-2710	5	16
β-strand	2712	1	15
α-helix	2722-2724	3
α-helix	2725-2728	4
β-strand	2733-2735	3	15
α-helix	2740-2755	16
α-helix	2763-2765	3
α-helix	2766-2783	18
α-helix	2796-2810	15
α-helix	2818-2829	12
α-helix	2830-2834	5
α-helix	2840-2857	18
α-helix	2863-2866	4
β-strand	2873	1	19
β-strand	2883	1	19
α-helix	2886-2901	16
α-helix	2913-2927	15
β-strand	2932-2936	5	20
α-helix	2946-2953	8
β-strand	2957-2960	4	20
α-helix	2969-2980	12
α-helix	2981-2985	5
β-strand	2990-2995	6	20
α-helix	2996-2998	3
α-helix	3005-3014	10
α-helix	3024-3040	17
α-helix	3047-3060	14
β-strand	3062-3068	7	20
α-helix	3083-3088	6
β-strand	3089-3093	5	20
α-helix	3099-3110	12
α-helix	3139-3164	26
α-helix	3173-3220	48
α-helix	3475-3516	42
α-helix	3522-3538	17
α-helix	3549-3552	4
α-helix	3556-3564	9
α-helix	3571-3581	11
α-helix	3586	1
β-strand	3587-3590	4	21
α-helix	3596-3603	8
α-helix	3605-3607	3
β-strand	3610	1	22
α-helix	3620-3629	10
β-strand	3633	1	22
α-helix	3645-3650	6
β-strand	3655	1	23
β-strand	3660	1	23
β-strand	3679-3680	2	21
α-helix	3690-3695	6
β-strand	3697-3700	4	21
α-helix	3705-3719	15
α-helix	3722-3732	11
α-helix	3737-3754	18
α-helix	3766-3785	20
α-helix	3789-3799	11
α-helix	3802-3817	16
α-helix	3818-3820	3
α-helix	3829-3841	13
α-helix	3852-3873	22
α-helix	3877-3879	3
α-helix	3880-3894	15
α-helix	3902-3910	9
α-helix	3916-3917	2
α-helix	3929-3938	10
α-helix	3942-3944	3
α-helix	3947-3953	7
α-helix	3957-3961	5
α-helix	3982-3996	15
α-helix	3998-4000	3
α-helix	4001-4013	13
α-helix	4027-4029	3
α-helix	4030-4034	5
β-strand	4041-4045	5	24
α-helix	4052-4061	10
β-strand	4066-4070	5	24
α-helix	4074-4090	17
β-strand	4093-4097	5	24
α-helix	4099-4101	3
α-helix	4103-4113	11
β-strand	4123-4129	7	24
α-helix	4136-4140	5
β-strand	4143	1	24
β-strand	4146-4147	2	24
α-helix	4153-4163	11
α-helix	4166-4170	5
α-helix	4175-4193	19
α-helix	4194-4196	3
α-helix	4209-4227	19
α-helix	4240-4246	7
α-helix	4247-4251	5
α-helix	4259-4272	14
α-helix	4275-4278	4
β-strand	4283-4288	6	25
β-strand	4292-4295	4	25
α-helix	4296-4297	2
α-helix	4302-4310	9
α-helix	4318-4321	4
α-helix	4327-4350	24
α-helix	4376-4390	15
α-helix	4397-4400	4
α-helix	4404-4406	3
α-helix	4408-4439	32
α-helix	4446-4457	12
α-helix	4459-4461	3
α-helix	4475-4499	25
β-strand	4508-4510	3	26
α-helix	4517-4532	16
α-helix	4536-4538	3
β-strand	4539-4545	7	26
β-strand	4557-4561	5	26
β-strand	4564-4571	8	27
β-strand	4574-4584	11	27
β-strand	4588-4594	7	26
α-helix	4598-4601	4
β-strand	4604-4610	7	27
β-strand	4618-4626	9	27
α-helix	4632-4638	7
β-strand	4641-4643	3	27

Chain E: 1 helix, 27 β-strands

Element	Residues	Length	Sheet
β-strand	96-104	9	28
β-strand	111-116	6	29
β-strand	123-127	5	29
β-strand	133-135	3	29
β-strand	142-145	4	29
β-strand	153-158	6	30
β-strand	165-169	5	30
β-strand	173-178	6	31
β-strand	183-189	7	31
β-strand	195-200	6	32
β-strand	207-211	5	32
β-strand	215-217	3	33
β-strand	229-231	3	33
β-strand	237-242	6	34
β-strand	249-253	5	34
β-strand	258-261	4	34
β-strand	270-272	3	34
α-helix	290-295	6
β-strand	311	1	35
β-strand	323	1	35
β-strand	330	1	35
β-strand	341-346	6	36
β-strand	353-357	5	36
β-strand	362-366	5	36
β-strand	371-376	6	36
β-strand	386-388	3	28
β-strand	394-397	4	28
β-strand	404-409	6	28

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	E	protein	411	Homo sapiens	P43034 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9E22_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 (E), FASTA

>9E22_2 Platelet-activating factor acetylhydrolase IB subunit beta (chains E)
GSVLSQRQRDELNRAIADYLRSNGYEEAYSVFKKEAELDVNEELDKKYAGLLEKKWTSVI
RLQKKVMELESKLNEAKEEFTSGGPLGQKRDPKEWIPRPPEKYALSGHRSPVTRVIFHPV
FSVMVSASEDATIKVWDYETGDFERTLKGHTDSVQDISFDHSGKLLASCSADMTIKLWDF
QGFECIRTMHGHDHNVSSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRM
VRPNQDGTLIASCSNDQTVRVWVVATKECKAELREHEHVVECISWAPESSYSSISEATGS
ETKKSGKPGPFLLSGSRDKTIKMWDVSTGMCLMTLVGHDNWVRGVLFHSGGKFILSCADD
KTLRVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGSVDQTVKVWECR

Ligands and cofactors

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

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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