8DYU: Human cytoplasmic dynein-1

Structure of human cytoplasmic dynein-1 bound to two Lis1 proteins. Determined by electron microscopy at 4.0 Å resolution. Released 1 Feb 2023.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 24,610
Mol. weight: 476.19 kDa
Ligands: ATP, ADP
Released: 1 Feb 2023

Explore 8DYU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DYU contains 139 α-helices and 121 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, 64 β-strands

Element	Residues	Length	Sheet
α-helix	1653-1655	3
α-helix	1705-1724	20
α-helix	1725-1727	3
α-helix	1735-1744	10
α-helix	1747-1767	21
α-helix	1776-1796	21
α-helix	1802-1827	26
α-helix	1836-1839	4
β-strand	1844-1846	3	1
α-helix	1853-1855	3
β-strand	1857-1860	4	1
β-strand	1865-1866	2	1
α-helix	1883-1897	15
β-strand	1901-1905	5	2
α-helix	1912-1923	12
α-helix	1926	1
β-strand	1927-1930	4	2
α-helix	1938-1951	14
β-strand	1954-1957	4	2
α-helix	1965-1986	22
β-strand	1999-2000	2	3
β-strand	2005-2006	2	3
β-strand	2013-2016	4	2
α-helix	2030-2033	4
β-strand	2036-2040	5	2
α-helix	2046-2057	12
α-helix	2062-2079	18
α-helix	2090-2110	21
α-helix	2133-2144	12
α-helix	2146-2148	3
α-helix	2154-2164	11
α-helix	2176-2186	11
α-helix	2201-2216	16
β-strand	2219-2223	5	4
α-helix	2230-2244	15
α-helix	2247-2248	2
β-strand	2249-2254	6	4
α-helix	2261-2265	5
β-strand	2266-2269	4	5
β-strand	2274-2277	4	5
α-helix	2279-2289	11
α-helix	2294-2296	3
β-strand	2298-2303	6	4
α-helix	2309-2312	4
α-helix	2313-2315	3
β-strand	2324-2326	3	6
β-strand	2332-2334	3	6
α-helix	2335-2336	2
β-strand	2340-2345	6	4
α-helix	2353-2356	4
β-strand	2360-2363	4	4
α-helix	2371-2384	14
α-helix	2411-2423	13
α-helix	2424-2426	3
α-helix	2433-2440	8
α-helix	2451-2475	25
α-helix	2480-2482	3
α-helix	2483-2502	20
α-helix	2508-2521	14
α-helix	2534-2536	3
β-strand	2537-2539	3	7
β-strand	2545-2547	3	7
α-helix	2548-2551	4
α-helix	2559-2561	3
α-helix	2572-2586	15
β-strand	2591-2594	4	8
α-helix	2601-2610	10
β-strand	2615-2620	6	8
α-helix	2628-2638	11
β-strand	2639-2644	6	9
β-strand	2647-2652	6	9
β-strand	2658-2663	6	8
α-helix	2678-2689	12
β-strand	2691-2694	4	9
β-strand	2699-2703	5	9
β-strand	2706-2712	7	8
α-helix	2721-2724	4
α-helix	2725-2728	4
β-strand	2733-2734	2	8
α-helix	2741-2755	15
α-helix	2760-2765	6
α-helix	2766-2781	16
α-helix	2797-2810	14
α-helix	2818-2832	15
α-helix	2840-2857	18
β-strand	2873-2874	2	10
β-strand	2882-2883	2	10
α-helix	2886-2903	18
α-helix	2913-2927	15
β-strand	2933-2937	5	11
α-helix	2945-2953	9
β-strand	2957-2959	3	11
α-helix	2969-2984	16
β-strand	2990-2994	5	11
α-helix	2996-2999	4
α-helix	3002-3014	13
α-helix	3024-3040	17
α-helix	3047-3061	15
β-strand	3063-3068	6	11
α-helix	3072-3081	10
α-helix	3083-3087	5
β-strand	3090-3095	6	11
α-helix	3099-3109	11
α-helix	3139-3164	26
α-helix	3173-3213	41
α-helix	3474-3481	8
α-helix	3483-3494	12
α-helix	3496-3501	6
α-helix	3503-3516	14
α-helix	3517-3519	3
α-helix	3522-3538	17
α-helix	3549-3553	5
α-helix	3556-3563	8
α-helix	3571-3581	11
α-helix	3586	1
β-strand	3587-3590	4	12
α-helix	3595-3603	9
α-helix	3605-3607	3
β-strand	3610-3613	4	12
α-helix	3619-3629	11
β-strand	3633-3636	4	12
α-helix	3638-3640	3
α-helix	3643-3645	3
α-helix	3646-3650	5
β-strand	3654-3655	2	13
β-strand	3660-3663	4	13
β-strand	3668-3670	3	13
β-strand	3677-3681	5	12
α-helix	3690-3695	6
β-strand	3697-3700	4	12
α-helix	3705-3720	16
α-helix	3722-3754	33
α-helix	3765-3775	11
α-helix	3776-3778	3
α-helix	3779-3793	15
α-helix	3795-3798	4
α-helix	3802-3816	15
α-helix	3829-3842	14
α-helix	3852-3872	21
α-helix	3877-3879	3
α-helix	3880-3891	12
α-helix	3902-3905	4
α-helix	3907-3910	4
α-helix	3929-3938	10
α-helix	3945-3948	4
α-helix	3950-3953	4
α-helix	3957-3961	5
α-helix	3982-3996	15
α-helix	3998-4000	3
α-helix	4001-4012	12
α-helix	4015-4017	3
α-helix	4027-4029	3
α-helix	4030-4034	5
β-strand	4041-4045	5	14
α-helix	4052-4062	11
β-strand	4066-4070	5	14
α-helix	4074-4090	17
β-strand	4093-4097	5	14
α-helix	4099-4101	3
α-helix	4103-4114	12
β-strand	4123-4129	7	14
α-helix	4136-4141	6
β-strand	4143-4147	5	14
α-helix	4149-4150	2
α-helix	4153-4163	11
α-helix	4166-4169	4
α-helix	4175-4195	21
α-helix	4209-4226	18
α-helix	4240-4246	7
α-helix	4247-4251	5
α-helix	4259-4272	14
α-helix	4275-4278	4
β-strand	4283	1	15
β-strand	4295	1	15
α-helix	4296-4297	2
α-helix	4302-4310	9
α-helix	4318-4320	3
α-helix	4327-4346	20
α-helix	4380-4394	15
α-helix	4408-4439	32
α-helix	4449-4457	9
α-helix	4459-4461	3
α-helix	4475-4497	23
α-helix	4503-4506	4
β-strand	4509-4510	2	16
α-helix	4517-4532	16
β-strand	4539	1	17
β-strand	4542-4544	3	16
β-strand	4559-4561	3	16
β-strand	4564-4566	3	18
β-strand	4569-4570	2	18
β-strand	4574-4576	3	18
β-strand	4588-4591	4	16
β-strand	4594	1	17
β-strand	4604-4610	7	18
β-strand	4618-4626	9	18
α-helix	4632-4638	7
β-strand	4641-4643	3	18

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	96-104	9	19
β-strand	111-116	6	20
β-strand	123-127	5	20
β-strand	131-136	6	20
β-strand	141-145	5	20
β-strand	153-158	6	21
β-strand	164-169	6	21
β-strand	173-178	6	21
β-strand	183-189	7	21
β-strand	195-200	6	22
β-strand	206-211	6	22
β-strand	216-220	5	22
β-strand	226-230	5	22
β-strand	237-242	6	23
β-strand	248-253	6	23
β-strand	258-262	5	23
β-strand	270-272	3	23
β-strand	279-284	6	24
α-helix	285-286	2
α-helix	289-296	8
β-strand	310-315	6	24
β-strand	319-324	6	24
β-strand	330-335	6	24
β-strand	341-346	6	25
β-strand	353-357	5	25
β-strand	361-366	6	25
β-strand	371-377	7	25
β-strand	383-388	6	19
β-strand	394-399	6	19
β-strand	404-409	6	19

Chain C: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	96-104	9	26
β-strand	111-116	6	27
β-strand	123-127	5	27
β-strand	132-135	4	27
β-strand	142-146	5	27
β-strand	153-158	6	28
β-strand	164-169	6	28
β-strand	174-178	5	28
β-strand	183-188	6	28
β-strand	195-200	6	29
β-strand	206-211	6	29
β-strand	215-220	6	29
β-strand	226-231	6	29
β-strand	239-242	4	30
β-strand	248-252	5	30
β-strand	258-262	5	30
β-strand	270-272	3	30
β-strand	279-281	3	31
β-strand	284	1	31
α-helix	285-286	2
α-helix	287-289	3
α-helix	290-296	7
β-strand	310-315	6	31
β-strand	319-324	6	31
β-strand	330-335	6	31
β-strand	341-346	6	32
β-strand	353-357	5	32
β-strand	362-366	5	32
β-strand	371-376	6	32
β-strand	385-388	4	26
β-strand	394-399	6	26
β-strand	403-409	7	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytoplasmic dynein 1 heavy chain 1	A	protein	3328	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

>8DYU_1 Cytoplasmic dynein 1 heavy chain 1 (chains A)
GQVALEELQDLKGVWSELSKVWEQIDQMKEQPWVSVQPRKLRQNLDALLNQLKSFPARLR
QYASYEFVQRLLKGYMKINMLVIELKSEALKDRHWKQLMKRLHVNWVVSELTLGQIWDVD
LQKNEAIVKDVLLVAQGEMALEEFLKQIREVWNTYELDLVNYQNKCRLIRGWDDLFNKVK
EHINSVSAMKLSPYYKVFEEDALSWEDKLNRIMALFDVWIDVQRRWVYLEGIFTGSADIK
HLLPVETQRFQSISTEFLALMKKVSKSPLVMDVLNIQGVQRSLERLADLLGKIQKALGEY
LERERSSFPRFYFVGDEDLLEIIGNSKNVAKLQKHFKKMFAGVSSIILNEDNSVVLGISS
REGEEVMFKTPVSITEHPKINEWLTLVEKEMRVTLAKLLAESVTEVEIFGKATSIDPNTY
ITWIDKYQAQLVVLSAQIAWSENVETALSSMGGGGDAAPLHSVLSNVEVTLNVLADSVLM
EQPPLRRRKLEHLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPKQTDVLQQLS
IQMANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEARLGGSPFGPAGTGKTESVKA
LGHQLGRFVLVFNCDETFDFQAMGRIFVGLCQVGAWGCFDEFNRLEERMLSAVSQQVQCI
QEALREHSNPNYDKTSAPITCELLNKQVKVSPDMAIFITMNPGYAGRSNLPDNLKKLFRS
LAMTKPDRQLIAQVMLYSQGFRTAEVLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLV
SAGNVKRERIQKIKREKEERGEAVDEGEIAENLPEQEILIQSVCETMVPKLVAEDIPLLF
SLLSDVFPGVQYHRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINH
GLMMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAISKDHLYGTLDPNTREWTDG
LFTHVLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSVLDDNKLLTLPNGERLSLPPN
VRIMFEVQDLKYATLATVSRCGMVWFSEDVLSTDMIFNNFLARLRSIPLDEGEDEAQRRR
KGKEDEGEEAASPMLQIQRDAATIMQPYFTSNGLVTKALEHAFQLEHIMDLTRLRCLGSL
FSMLHQACRNVAQYNANHPDFPMQIEQLERYIQRYLVYAILWSLSGDSRLKMRAELGEYI
RRITTVPLPTAPNIPIIDYEVSISGEWSPWQAKVPQIEVETHKVAAPDVVVPTLDTVRHE
ALLYTWLAEHKPLVLCGPPGSGKTMTLFSALRALPDMEVVGLNFSSATTPELLLKTFDHY
CEYRRTPNGVVLAPVQLGKWLVLFCDEINLPDMDKYGTQRVISFIRQMVEHGGFYRTSDQ
TWVKLERIQFVGACNPPTDPGRKPLSHRFLRHVPVVYVDYPGPASLTQIYGTFNRAMLRL
IPSLRTYAEPLTAAMVEFYTMSQERFTQDTQPHYIYSPREMTRWVRGIFEALRPLETLPV
EGLIRIWAHEALRLFQDRLVEDEERRWTDENIDTVALKHFPNIDREKAMSRPILYSNWLS
KDYIPVDQEELRDYVKARLKVFYEEELDVPLVLFNEVLDHVLRIDRIFRQPQGHLLLIGV
SGAGKTTLSRFVAWMNGLSVYQIKVHRKYTGEDFDEDLRTVLRRSGCKNEKIAFIMDESN
VLDSGFLERMNTLLANGEVPGLFEGDEYATLMTQCKEGAQKEGLMLDSHEELYKWFTSQV
IRNLHVVFTMNPSSEGLKDRAATSPALFNRCVLNWFGDWSTEALYQVGKEFTSKMDLEKP
NYIVPDYMPVVYDKLPQPPSHREAIVNSCVFVHQTLHQANARLAKRGGRTMAITPRHYLD
FINHYANLFHEKRSELEEQQMHLNVGLRKIKETVDQVEELRRDLRIKSQELEVKNAAAND
KLKKMVKDQQEAEKKKVMSQEIQEQLHKQQEVIADKQMSVKEDLDKVEPAVIEAQNAVKS
IKKQHLVEVRSMANPPAAVKLALESICLLLGESTTDWKQIRSIIMRENFIPTIVNFSAEE
ISDAIREKMKKNYMSNPSYNYEIVNRASLACGPMVKWAIAQLNYADMLKRVEPLRNELQK
LEDDAKDNQQKANEVEQMIRDLEASIARYKEEYAVLISEAQAIKADLAAVEAKVNRSTAL
LKSLSAERERWEKTSETFKNQMSTIAGDCLLSAAFIAYAGYFDQQMRQNLFTTWSHHLQQ
ANIQFRTDIARTEYLSNADERLRWQASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATE
FIMNEYKDRKITRTSFLDDAFRKNLESALRFGNPLLVQDVESYDPVLNPVLNREVRRTGG
RVLITLGDQDIDLSPSFVIFLSTRDPTVEFPPDLCSRVTFVNFTVTRSSLQSQCLNEVLK
AERPDVDEKRSDLLKLQGEFQLRLRQLEKSLLQALNEVKGRILDDDTIITTLENLKREAA
EVTRKVEETDIVMQEVETVSQQYLPLSTACSSIYFTMESLKQIHFLYQYSLQFFLDIYHN
VLYENPNLKGVTDHTQRLSIITKDLFQVAFNRVARGMLHQDHITFAMLLARIKLKGTVGE
PTYDAEFQHFLRGNEIVLSAGSTPRIQGLTVEQAEAVVRLSCLPAFKDLIAKVQADEQFG
IWLDSSSPEQTVPYLWSEETPATPIGQAIHRLLLIQAFRPDRLLAMAHMFVSTNLGESFM
SIMEQPLDLTHIVGTEVKPNTPVLMCSVPGYDASGHVEDLAAEQNTQITSIAIGSAEGFN
QADKAINTAVKSGRWVMLKNVHLAPGWLMQLEKKLHSLQPHACFRLFLTMEINPKVPVNL
LRAGRIFVFEPPPGVKANMLRTFSSIPVSRICKSPNERARLYFLLAWFHAIIQERLRYAP
LGWSKKYEFGESDLRSACDTVDTWLDDTAKGRQNISPDKIPWSALKTLMAQSIYGGRVDN
EFDQRLLNTFLERLFTTRSFDSEFKLACKVDGHKDIQMPDGIRREEFVQWVELLPDTQTP
SWLGLPNNAERVLLTTQGVDMISKMLKMQMLEDEDDLAYAETEKKTRTDSTSDGRPAWMR
TLHTTASNWLHLIPQTLSHLKRTVENIKDPLFRFFEREVKMGAKLLQDVRQDLADVVQVC
EGKKKQTNYLRTLINELVKGILPRSWSHYTVPAGMTVIQWVSDFSERIKQLQNISLAAAS
GGAKELKNIHVCLGGLFVPEAYITATRQYVAQANSWSLEELCLEVNVTTSQGATLDACSF
GVTGLKLQGATCNNNKLSLSNAISTALPLTQLRWVKQTNTEKKASVVTLPVYLNFTRADL
IFTVDFEIATKEDPRSFYERGVAVLCTE

Sequence of entity 2 (B, C), FASTA

>8DYU_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
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3

Primary citation

Structures of human dynein in complex with the lissencephaly 1 protein, LIS1. Reimer, J.M., DeSantis, M.E., Reck-Peterson, S.L. et al. Elife (2023) 12. DOI 10.7554/eLife.84302 · 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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