8PQY: Cytoplasmic dynein-1 motor domain

Cytoplasmic dynein-1 motor domain bound to LIS1. Determined by electron microscopy at 3.8 Å resolution. Released 27 Mar 2024.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 27,916
Mol. weight: 628.31 kDa
Ligands: ADP, MG, ATP
Released: 27 Mar 2024

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

Secondary structure: helices and β-sheets

8PQY contains 137 α-helices and 133 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: 135 helices, 73 β-strands

Element	Residues	Length	Sheet
α-helix	1445-1471	27
β-strand	1474	1	1
β-strand	1476-1480	5	2
β-strand	1484-1488	5	2
α-helix	1490-1509	20
α-helix	1517-1553	37
α-helix	1562-1584	23
β-strand	1587	1	1
α-helix	1588-1592	5
α-helix	1597-1615	19
α-helix	1617-1623	7
α-helix	1628-1631	4
α-helix	1634-1642	9
α-helix	1650-1652	3
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	1692-1694	3
α-helix	1698-1727	30
α-helix	1735-1744	10
α-helix	1747-1767	21
α-helix	1776-1796	21
α-helix	1802-1826	25
α-helix	1836-1839	4
β-strand	1843-1846	4	4
α-helix	1853-1855	3
β-strand	1857-1861	5	4
β-strand	1864-1866	3	4
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	1966-1985	20
β-strand	1998-2001	4	6
β-strand	2004-2007	4	6
β-strand	2013-2018	6	5
α-helix	2025-2029	5
α-helix	2030-2035	6
β-strand	2036-2040	5	5
α-helix	2046-2057	12
α-helix	2062-2079	18
α-helix	2081-2082	2
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	2219-2223	5	7
α-helix	2230-2245	16
β-strand	2249-2254	6	7
α-helix	2261-2265	5
β-strand	2268	1	8
β-strand	2275	1	8
α-helix	2279-2289	11
β-strand	2298-2303	6	7
α-helix	2312-2314	3
β-strand	2324-2325	2	9
β-strand	2333-2334	2	9
β-strand	2339-2344	6	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	10
β-strand	2545-2547	3	10
α-helix	2548-2551	4
α-helix	2572-2586	15
β-strand	2591-2594	4	11
α-helix	2601-2611	11
β-strand	2615-2620	6	11
α-helix	2628-2638	11
β-strand	2639-2644	6	12
β-strand	2647-2652	6	12
β-strand	2658-2663	6	11
α-helix	2670-2671	2
α-helix	2678-2688	11
β-strand	2691-2694	4	12
β-strand	2699-2703	5	12
β-strand	2706-2712	7	11
α-helix	2722-2724	3
α-helix	2725-2728	4
β-strand	2733-2735	3	11
α-helix	2741-2755	15
α-helix	2763-2765	3
α-helix	2766-2780	15
α-helix	2796-2809	14
α-helix	2818-2833	16
α-helix	2840-2857	18
α-helix	2863-2866	4
β-strand	2873-2874	2	13
β-strand	2882-2883	2	13
α-helix	2886-2900	15
α-helix	2913-2927	15
β-strand	2933-2936	4	14
α-helix	2943-2953	11
β-strand	2957-2960	4	14
α-helix	2969-2980	12
α-helix	2981-2985	5
β-strand	2990-2995	6	14
α-helix	3002-3013	12
α-helix	3024-3040	17
α-helix	3048-3061	14
β-strand	3062-3068	7	14
α-helix	3074-3081	8
α-helix	3084-3087	4
β-strand	3090-3093	4	14
α-helix	3099-3109	11
α-helix	3121-3123	3
α-helix	3139-3164	26
α-helix	3166-3168	3
α-helix	3173-3239	67
α-helix	3451-3501	51
α-helix	3503-3515	13
α-helix	3522-3538	17
α-helix	3549-3553	5
α-helix	3556-3564	9
α-helix	3571-3581	11
α-helix	3586	1
β-strand	3587-3590	4	15
α-helix	3595-3603	9
α-helix	3609	1
β-strand	3610-3613	4	15
α-helix	3620-3629	10
β-strand	3633-3636	4	15
α-helix	3638-3640	3
α-helix	3643-3645	3
α-helix	3646-3649	4
β-strand	3654-3656	3	16
β-strand	3659-3664	6	16
β-strand	3667-3670	4	16
β-strand	3677-3681	5	15
α-helix	3690-3695	6
β-strand	3697-3700	4	15
α-helix	3702-3704	3
α-helix	3705-3720	16
α-helix	3722-3753	32
α-helix	3765-3817	53
α-helix	3819-3822	4
α-helix	3829-3840	12
α-helix	3852-3872	21
α-helix	3877-3879	3
α-helix	3880-3893	14
α-helix	3902-3909	8
α-helix	3929-3938	10
α-helix	3947-3953	7
α-helix	3982-3996	15
α-helix	3998-4000	3
α-helix	4001-4012	12
α-helix	4027-4029	3
α-helix	4030-4034	5
β-strand	4041-4045	5	17
α-helix	4052-4061	10
β-strand	4068-4070	3	17
α-helix	4074-4089	16
β-strand	4094-4097	4	17
α-helix	4099-4101	3
α-helix	4103-4114	12
β-strand	4124-4129	6	17
α-helix	4136-4141	6
β-strand	4143-4147	5	17
α-helix	4149-4150	2
α-helix	4153-4163	11
α-helix	4166-4169	4
α-helix	4176-4192	17
α-helix	4210-4226	17
α-helix	4235-4237	3
α-helix	4240-4246	7
α-helix	4247-4251	5
α-helix	4259-4272	14
α-helix	4275-4278	4
β-strand	4283-4285	3	18
β-strand	4294-4295	2	18
α-helix	4296-4297	2
α-helix	4302-4309	8
α-helix	4318-4321	4
α-helix	4329-4346	18
α-helix	4380-4390	11
α-helix	4391-4394	4
α-helix	4408-4438	31
α-helix	4446-4457	12
β-strand	4459	1	19
α-helix	4460-4461	2
β-strand	4474	1	19
α-helix	4475-4496	22
α-helix	4504-4506	3
β-strand	4508-4510	3	20
α-helix	4511-4513	3
α-helix	4517-4532	16
β-strand	4540-4544	5	20
β-strand	4558-4561	4	20
β-strand	4563-4564	2	21
β-strand	4568-4570	3	21
β-strand	4574-4577	4	21
β-strand	4584-4585	2	21
β-strand	4588-4593	6	20
β-strand	4604-4610	7	21
β-strand	4618-4626	9	21
α-helix	4632-4637	6
β-strand	4642-4643	2	21

Chain B: 1 helix, 30 β-strands

Element	Residues	Length	Sheet
β-strand	96	1	22
β-strand	102-105	4	23
β-strand	111-116	6	24
β-strand	123-127	5	24
β-strand	132-136	5	24
β-strand	141-146	6	24
β-strand	153-157	5	25
β-strand	164-169	6	25
β-strand	173-178	6	25
β-strand	183-189	7	25
β-strand	199	1	26
β-strand	206-210	5	26
β-strand	215-220	6	26
β-strand	226-231	6	26
β-strand	237-242	6	27
β-strand	248-253	6	27
β-strand	258-262	5	27
β-strand	268-272	5	27
β-strand	279-284	6	28
α-helix	287-294	8
β-strand	310-315	6	28
β-strand	319-324	6	28
β-strand	329-335	7	28
β-strand	341-346	6	29
β-strand	352-357	6	29
β-strand	361-366	6	29
β-strand	371-376	6	29
β-strand	383-388	6	23
β-strand	394-399	6	23
β-strand	403-408	6	23
β-strand	409	1	22

Chain C: 1 helix, 30 β-strands

Element	Residues	Length	Sheet
β-strand	96	1	30
β-strand	102-105	4	31
β-strand	111-116	6	32
β-strand	123-127	5	32
β-strand	132-136	5	32
β-strand	141-146	6	32
β-strand	155-157	3	33
β-strand	164-168	5	33
β-strand	173-178	6	33
β-strand	184-189	6	33
β-strand	195-200	6	34
β-strand	206-211	6	34
β-strand	215-220	6	34
β-strand	226-231	6	34
β-strand	237-242	6	35
β-strand	248-253	6	35
β-strand	258-262	5	35
β-strand	268-272	5	35
β-strand	279-284	6	36
α-helix	290-296	7
β-strand	310-315	6	36
β-strand	319-324	6	36
β-strand	330-335	6	36
β-strand	341-346	6	37
β-strand	352-357	6	37
β-strand	361-366	6	37
β-strand	371-377	7	37
β-strand	383-388	6	31
β-strand	394-399	6	31
β-strand	403-408	6	31
β-strand	409	1	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytoplasmic dynein 1 heavy chain 1	A	protein	4646	Homo sapiens	Q14204
Platelet-activating factor acetylhydrolase IB subunit beta	B, C	protein	410	Homo sapiens	P43034 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8PQY_1 Cytoplasmic dynein 1 heavy chain 1 (chains A)
MSEPGGGGGEDGSAGLEVSAVQNVADVSVLQKHLRKLVPLLLEDGGEAPAALEAALEEKS
ALEQMRKFLSDPQVHTVLVERSTLKEDVGDEGEEEKEFISYNINIDIHYGVKSNSLAFIK
RTPVIDADKPVSSQLRVLTLSEDSPYETLHSFISNAVAPFFKSYIRESGKADRDGDKMAP
SVEKKIAELEMGLLHLQQNIEIPEISLPIHPMITNVAKQCYERGEKPKVTDFGDKVEDPT
FLNQLQSGVNRWIREIQKVTKLDRDPASGTALQEISFWLNLERALYRIQEKRESPEVLLT
LDILKHGKRFHATVSFDTDTGLKQALETVNDYNPLMKDFPLNDLLSATELDKIRQALVAI
FTHLRKIRNTKYPIQRALRLVEAISRDLSSQLLKVLGTRKLMHVAYEEFEKVMVACFEVF
QTWDDEYEKLQVLLRDIVKRKREENLKMVWRINPAHRKLQARLDQMRKFRRQHEQLRAVI
VRVLRPQVTAVAQQNQGEVPEPQDMKVAEVLFDAADANAIEEVNLAYENVKEVDGLDVSK
EGTEAWEAAMKRYDERIDRVETRITARLRDQLGTAKNANEMFRIFSRFNALFVRPHIRGA
IREYQTQLIQRVKDDIESLHDKFKVQYPQSQACKMSHVRDLPPVSGSIIWAKQIDRQLTA
YMKRVEDVLGKGWENHVEGQKLKQDGDSFRMKLNTQEIFDDWARKVQQRNLGVSGRIFTI
ESTRVRGRTGNVLKLKVNFLPEIITLSKEVRNLKWLGFRVPLAIVNKAHQANQLYPFAIS
LIESVRTYERTCEKVEERNTISLLVAGLKKEVQALIAEGIALVWESYKLDPYVQRLAETV
FNFQEKVDDLLIIEEKIDLEVRSLETCMYDHKTFSEILNRVQKAVDDLNLHSYSNLPIWV
NKLDMEIERILGVRLQAGLRAWTQVLLGQAEDKAEVDMDTDAPQVSHKPGGEPKIKNVVH
ELRITNQVIYLNPPIEECRYKLYQEMFAWKMVVLSLPRIQSQRYQVGVHYELTEEEKFYR
NALTRMPDGPVALEESYSAVMGIVSEVEQYVKVWLQYQCLWDMQAENIYNRLGEDLNKWQ
ALLVQIRKARGTFDNAETKKEFGPVVIDYGKVQSKVNLKYDSWHKEVLSKFGQMLGSNMT
EFHSQISKSRQELEQHSVDTASTSDAVTFITYVQSLKRKIKQFEKQVELYRNGQRLLEKQ
RFQFPPSWLYIDNIEGEWGAFNDIMRRKDSAIQQQVANLQMKIVQEDRAVESRTTDLLTD
WEKTKPVTGNLRPEEALQALTIYEGKFGRLKDDREKCAKAKEALELTDTGLLSGSEERVQ
VALEELQDLKGVWSELSKVWEQIDQMKEQPWVSVQPRKLRQNLDALLNQLKSFPARLRQY
ASYEFVQRLLKGYMKINMLVIELKSEALKDRHWKQLMKRLHVNWVVSELTLGQIWDVDLQ
KNEAIVKDVLLVAQGEMALEEFLKQIREVWNTYELDLVNYQNKCRLIRGWDDLFNKVKEH
INSVSAMKLSPYYKVFEEDALSWEDKLNRIMALFDVWIDVQRRWVYLEGIFTGSADIKHL
LPVETQEFQSISTEFLALMKKVSKSPLVMDVLNIQGVQRSLERLADLLGEIQKALGEYLE
RERSSFPRFYFVGDEDLLEIIGNSKNVAKLQKHFKKMFAGVSSIILNEDNSVVLGISSRE
GEEVMFKTPVSITEHPKINEWLTLVEKEMRVTLAKLLAESVTEVEIFGKATSIDPNTYIT
WIDKYQAQLVVLSAQIAWSENVETALSSMGGGGDAAPLHSVLSNVEVTLNVLADSVLMEQ
PPLRRRKLEHLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPKQTDVLQQLSIQ
MANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEARLGGSPFGPAGTGKTESVKALG
HQLGRFVLVFNCDETFDFQAMGRIFVGLCQVGAWGCFDEFNRLEERMLSAVSQQVQCIQE
ALREHSNPNYDKTSAPITCELLNKQVKVSPDMAIFITMNPGYAGRSNLPDNLKKLFRSLA
MTKPDRQLIAQVMLYSQGFRTAEVLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLVSA
GNVKRERIQKIKREKEERGEAVDEGEIAENLPEQEILIQSVCETMVPKLVAEDIPLLFSL
LSDVFPGVQYHRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINHGL
MMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAISKDHLYGTLDPNTREWTDGLF
THVLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSVLDDNKLLTLPNGERLSLPPNVR
IMFEVQDLKYATLATVSRCGMVWFSEDVLSTDMIFNNFLARLRSIPLDEGEDEAQRRRKG
KEDEGEEAASPMLQIQRDAATIMQPYFTSNGLVTKALEHAFQLEHIMDLTRLRCLGSLFS
MLHQACRNVAQYNANHPDFPMQIEQLERYIQRYLVYAILWSLSGDSRLKMRAELGEYIRR
ITTVPLPTAPNIPIIDYEVSISGEWSPWQAKVPQIEVETHKVAAPDVVVPTLDTVRHEAL
LYTWLAEHKPLVLCGPPGSGKTMTLFSALRALPDMEVVGLNFSSATTPELLLKTFDHYCE
YRRTPNGVVLAPVQLGKWLVLFCDEINLPDMDKYGTQRVISFIRQMVEHGGFYRTSDQTW
VKLERIQFVGACNPPTDPGRKPLSHRFLRHVPVVYVDYPGPASLTQIYGTFNRAMLRLIP
SLRTYAEPLTAAMVEFYTMSQERFTQDTQPHYIYSPREMTRWVRGIFEALRPLETLPVEG
LIRIWAHEALRLFQDRLVEDEERRWTDENIDTVALKHFPNIDREKAMSRPILYSNWLSKD
YIPVDQEELRDYVKARLKVFYEEELDVPLVLFNEVLDHVLRIDRIFRQPQGHLLLIGVSG
AGKTTLSRFVAWMNGLSVYQIKVHRKYTGEDFDEDLRTVLRRSGCKNEKIAFIMDESNVL
DSGFLERMNTLLANGEVPGLFEGDEYATLMTQCKEGAQKEGLMLDSHEELYKWFTSQVIR
NLHVVFTMNPSSEGLKDRAATSPALFNRCVLNWFGDWSTEALYQVGKEFTSKMDLEKPNY
IVPDYMPVVYDKLPQPPSHREAIVNSCVFVHQTLHQANARLAKRGGRTMAITPRHYLDFI
NHYANLFHEKRSELEEQQMHLNVGLRKIKETVDQVEELRRDLRIKSQELEVKNAAANDKL
KKMVKDQQEAEKKKVMSQEIQEQLHKQQEVIADKQMSVKEDLDKVEPAVIEAQNAVKSIK
KQHLVEVRSMANPPAAVKLALESICLLLGESTTDWKQIRSIIMRENFIPTIVNFSAEEIS
DAIREKMKKNYMSNPSYNYEIVNRASLACGPMVKWAIAQLNYADMLKRVEPLRNELQKLE
DDAKDNQQKANEVEQMIRDLEASIARYKEEYAVLISEAQAIKADLAAVEAKVNRSTALLK
SLSAERERWEKTSETFKNQMSTIAGDCLLSAAFIAYAGYFDQQMRQNLFTTWSHHLQQAN
IQFRTDIARTEYLSNADERLRWQASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATEFI
MNEYKDRKITRTSFLDDAFRKNLESALRFGNPLLVQDVESYDPVLNPVLNREVRRTGGRV
LITLGDQDIDLSPSFVIFLSTRDPTVEFPPDLCSRVTFVNFTVTRSSLQSQCLNEVLKAE
RPDVDEKRSDLLKLQGEFQLRLRQLEKSLLQALNEVKGRILDDDTIITTLENLKREAAEV
TRKVEETDIVMQEVETVSQQYLPLSTACSSIYFTMESLKQIHFLYQYSLQFFLDIYHNVL
YENPNLKGVTDHTQRLSIITKDLFQVAFNRVARGMLHQDHITFAMLLARIKLKGTVGEPT
YDAEFQHFLRGNEIVLSAGSTPRIQGLTVEQAEAVVRLSCLPAFKDLIAKVQADEQFGIW
LDSSSPEQTVPYLWSEETPATPIGQAIHRLLLIQAFRPDRLLAMAHMFVSTNLGESFMSI
MEQPLDLTHIVGTEVKPNTPVLMCSVPGYDASGHVEDLAAEQNTQITSIAIGSAEGFNQA
DKAINTAVKSGRWVMLKNVHLAPGWLMQLEKKLHSLQPHACFRLFLTMEINPKVPVNLLR
AGRIFVFEPPPGVKANMLRTFSSIPVSRICKSPNERARLYFLLAWFHAIIQERLRYAPLG
WSKKYEFGESDLRSACDTVDTWLDDTAKGRQNISPDKIPWSALKTLMAQSIYGGRVDNEF
DQRLLNTFLERLFTTRSFDSEFKLACKVDGHKDIQMPDGIRREEFVQWVELLPDTQTPSW
LGLPNNAERVLLTTQGVDMISKMLKMQMLEDEDDLAYAETEKKTRTDSTSDGRPAWMRTL
HTTASNWLHLIPQTLSHLKRTVENIKDPLFRFFEREVKMGAKLLQDVRQDLADVVQVCEG
KKKQTNYLRTLINELVKGILPRSWSHYTVPAGMTVIQWVSDFSERIKQLQNISLAAASGG
AKELKNIHVCLGGLFVPEAYITATRQYVAQANSWSLEELCLEVNVTTSQGATLDACSFGV
TGLKLQGATCNNNKLSLSNAISTALPLTQLRWVKQTNTEKKASVVTLPVYLNFTRADLIF
TVDFEIATKEDPRSFYERGVAVLCTE

Sequence of entity 2 (B, C), FASTA

>8PQY_2 Platelet-activating factor acetylhydrolase IB subunit beta (chains B, C)
MVLSQRQRDELNRAIADYLRSNGYEEAYSVFKKEAELDVNEELDKKYAGLLEKKWTSVIR
LQKKVMELESKLNEAKEEFTSGGPLGQKRDPKEWIPRPPEKYALSGHRSPVTRVIFHPVF
SVMVSASEDATIKVWDYETGDFERTLKGHTDSVQDISFDHSGKLLASCSADMTIKLWDFQ
GFECIRTMHGHDHNVSSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRMV
RPNQDGTLIASCSNDQTVRVWVVATKECKAELREHEHVVECISWAPESSYSSISEATGSE
TKKSGKPGPFLLSGSRDKTIKMWDVSTGMCLMTLVGHDNWVRGVLFHSGGKFILSCADDK
TLRVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGSVDQTVKVWECR

Ligands and cofactors

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

Primary citation

Molecular mechanism of dynein-dynactin complex assembly by LIS1. Singh, K., Lau, C.K., Manigrasso, G. et al. Science (2024) 383:eadk8544-eadk8544. DOI 10.1126/science.adk8544 · 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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