9BN3: Cytoplasmic dynein 1 heavy chain 1

The alpha registry-locked dynein motor domain mutant in 5mM ATP condition, class1. Determined by electron microscopy at 2.8 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 23,152
Mol. weight: 534.86 kDa
Ligands: ADP, ATP
Released: 23 Apr 2025

Explore 9BN3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BN3 contains 141 α-helices and 77 β-strands across 1 chain. 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: 141 helices, 77 β-strands

Element	Residues	Length	Sheet
α-helix	1466-1469	4
β-strand	1474	1	1
β-strand	1477-1478	2	2
β-strand	1486-1487	2	2
α-helix	1491-1509	19
α-helix	1521-1553	33
α-helix	1562-1584	23
β-strand	1587	1	1
α-helix	1588-1592	5
α-helix	1597-1624	28
α-helix	1627-1631	5
α-helix	1634-1642	9
α-helix	1647-1652	6
α-helix	1654-1657	4
β-strand	1663-1666	4	3
β-strand	1672-1677	6	3
β-strand	1684-1691	8	3
α-helix	1698-1729	32
α-helix	1735-1744	10
α-helix	1747-1772	26
α-helix	1777-1796	20
α-helix	1802-1827	26
α-helix	1836-1839	4
β-strand	1843-1846	4	4
β-strand	1857-1860	4	4
β-strand	1866-1867	2	4
α-helix	1868	1
α-helix	1883-1897	15
β-strand	1901-1905	5	5
α-helix	1912-1922	11
β-strand	1927-1931	5	5
α-helix	1938-1951	14
β-strand	1954-1958	5	5
α-helix	1960-1962	3
α-helix	1965-1983	19
α-helix	1984-1986	3
α-helix	1996-1997	2
β-strand	1998-2000	3	6
β-strand	2005-2007	3	6
β-strand	2015-2016	2	5
β-strand	2036-2040	5	5
α-helix	2046-2056	11
α-helix	2062-2076	15
α-helix	2081-2082	2
α-helix	2090-2112	23
α-helix	2133-2145	13
α-helix	2153-2164	12
α-helix	2176-2185	10
α-helix	2201-2216	16
β-strand	2221-2223	3	7
β-strand	2226	1	8
β-strand	2228	1	8
α-helix	2230-2245	16
β-strand	2248-2251	4	9
α-helix	2261-2265	5
β-strand	2266-2268	3	10
β-strand	2275-2277	3	10
α-helix	2279-2288	10
β-strand	2297-2302	6	9
β-strand	2305	1	7
α-helix	2309-2312	4
α-helix	2316-2319	4
β-strand	2324-2326	3	11
β-strand	2332-2334	3	11
α-helix	2335-2336	2
β-strand	2340-2342	3	9
β-strand	2345	1	7
α-helix	2353-2357	5
β-strand	2361-2363	3	7
α-helix	2371-2384	14
α-helix	2411-2423	13
α-helix	2431-2441	11
α-helix	2451-2475	25
α-helix	2483-2502	20
α-helix	2508-2519	12
α-helix	2534-2536	3
β-strand	2537-2538	2	12
β-strand	2546-2547	2	12
α-helix	2548-2551	4
α-helix	2559-2561	3
α-helix	2572-2586	15
β-strand	2591-2594	4	13
α-helix	2601-2609	9
β-strand	2615-2621	7	13
α-helix	2628-2638	11
β-strand	2639-2642	4	14
β-strand	2648-2652	5	14
β-strand	2658-2664	7	13
α-helix	2670-2672	3
α-helix	2678-2688	11
β-strand	2691-2693	3	14
β-strand	2700-2703	4	14
β-strand	2706-2712	7	13
α-helix	2721-2724	4
α-helix	2725-2728	4
β-strand	2733-2735	3	13
α-helix	2737-2740	4
α-helix	2741-2755	15
α-helix	2756-2758	3
α-helix	2760-2765	6
α-helix	2766-2782	17
α-helix	2796-2808	13
α-helix	2818-2833	16
α-helix	2840-2857	18
α-helix	2863-2865	3
β-strand	2873	1	15
β-strand	2883	1	15
α-helix	2886-2903	18
α-helix	2913-2927	15
β-strand	2932-2937	6	16
α-helix	2943-2953	11
β-strand	2957-2960	4	16
α-helix	2969-2984	16
α-helix	2985-2987	3
β-strand	2990-2995	6	16
α-helix	3002-3013	12
α-helix	3024-3039	16
α-helix	3047-3060	14
β-strand	3062-3068	7	16
α-helix	3072-3081	10
α-helix	3083-3086	4
β-strand	3089-3094	6	16
α-helix	3095-3098	4
α-helix	3099-3109	11
α-helix	3140-3163	24
α-helix	3173-3219	47
α-helix	3472-3516	45
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	17
α-helix	3595-3603	9
α-helix	3609	1
β-strand	3610-3613	4	17
α-helix	3619-3629	11
β-strand	3633-3636	4	17
α-helix	3638-3640	3
α-helix	3643-3645	3
α-helix	3646-3650	5
β-strand	3654	1	18
β-strand	3661-3662	2	18
β-strand	3669-3670	2	18
β-strand	3677-3681	5	17
α-helix	3690-3693	4
β-strand	3697-3700	4	17
α-helix	3705-3719	15
α-helix	3722-3733	12
α-helix	3737-3756	20
α-helix	3764-3785	22
α-helix	3794-3800	7
α-helix	3802-3817	16
α-helix	3829-3841	13
α-helix	3852-3872	21
α-helix	3880-3894	15
α-helix	3902-3910	9
α-helix	3911-3913	3
α-helix	3929-3940	12
α-helix	3942-3944	3
α-helix	3948-3952	5
α-helix	3956-3961	6
α-helix	3982-3995	14
α-helix	3998-4000	3
α-helix	4001-4013	13
α-helix	4019-4022	4
α-helix	4024-4025	2
α-helix	4027-4034	8
α-helix	4040	1
β-strand	4041-4045	5	19
α-helix	4052-4062	11
β-strand	4066-4070	5	19
α-helix	4074-4088	15
β-strand	4093-4097	5	19
α-helix	4099-4101	3
α-helix	4103-4112	10
β-strand	4125-4129	5	19
α-helix	4136-4141	6
β-strand	4143-4144	2	19
β-strand	4147	1	19
α-helix	4149-4150	2
α-helix	4153-4163	11
α-helix	4166-4170	5
α-helix	4175-4192	18
α-helix	4209-4226	18
α-helix	4235-4237	3
α-helix	4240-4249	10
α-helix	4259-4272	14
α-helix	4275-4278	4
β-strand	4283-4288	6	20
β-strand	4292-4295	4	20
α-helix	4296-4297	2
α-helix	4302-4310	9
α-helix	4318-4321	4
α-helix	4327-4345	19
α-helix	4377-4390	14
α-helix	4408-4439	32
α-helix	4446-4456	11
β-strand	4459	1	21
α-helix	4462-4464	3
β-strand	4474	1	21
α-helix	4475-4498	24
β-strand	4509-4510	2	22
α-helix	4511-4513	3
α-helix	4517-4531	15
β-strand	4539-4545	7	22
α-helix	4551-4553	3
β-strand	4557-4561	5	22
β-strand	4564-4566	3	23
β-strand	4568-4570	3	23
β-strand	4574-4577	4	23
β-strand	4583-4584	2	23
β-strand	4588-4594	7	22
α-helix	4599-4601	3
β-strand	4604-4610	7	23
β-strand	4618-4626	9	23
α-helix	4632-4637	6
β-strand	4641-4643	3	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytoplasmic dynein 1 heavy chain 1	A	protein	4646	Homo sapiens	Q14204

Sequence of entity 1 (A), FASTA

>9BN3_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
LPVETQRFQSISTEFLALMKKVSKSPLVMDVLNIQGVQRSLERLADLLGKIQKALGEYLE
RERSSFPRFYFVGDEDLLEIIGNSKNVAKLQKHFKKMFAGVSSIILNEDNSVVLGISSRE
GEEVMFKTPVSITEHPKINEWLTLVEKEMRVTLAKLLAESVTEVEIFGKATSIDPNTYIT
WIDKYQAQLVVLSAQIAWSENVETALSSMGGGGDAAPLHSVLSNVEVTLNVLADSVLMEQ
PPLRRRKLEHLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPKQTDVLQQLSIQ
MANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEARLGGSPFGPAGTGKTESVKALG
HQLGRFVLVFNCDETFDFQAMGRIFVGLCQVGAWGCFDEFNRLEERMLSAVSQQVQCIQE
ALREHSNPNYDKTSAPITCELLNKQVKVSPDMAIFITMNPGYAGRSNLPDNLKKLFRSLA
MTKPDRQLIAQVMLYSQGFRTAEVLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLVSA
GNVKRERIQKIKREKEERGEAVDEGEIAENLPEQEILIQSVCETMVPKLVAEDIPLLFSL
LSDVFPGVQYHRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINHGL
MMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAISKDHLYGTLDPNTREWTDGLF
THVLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSVLDDNKLLTLPNGERLSLPPNVR
IMFEVQDLKYATLATVSRCGMVWFSEDVLSTDMIFNNFLARLRSIPLDDGEDEAQRRRKG
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

Ligands and cofactors

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

Primary citation

The mechanochemical cycle of reactive full-length human dynein 1. Chai, P., Yang, J., Geohring, I.C. et al. Nat Struct Mol Biol (2025) 32:1383-1395. DOI 10.1038/s41594-025-01543-3 · 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
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
9BMY 2.86 Å, State-1 of motor domain from full-length human dynein-1 in apo condition

Browse structure collections

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