8FCY: PDB entry 8FCY

Engineered human dynein motor domain in microtubule-bound state. Determined by electron microscopy at 3.4 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Homo sapiens, Thermus thermophilus
Chains: 1
Atoms: 23,142
Mol. weight: 359.72 kDa
Ligands: ATP, ADP
Released: 21 Jun 2023

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

Secondary structure: helices and β-sheets

8FCY contains 147 α-helices and 69 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: 147 helices, 69 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
β-strand	22-24	3	1
β-strand	30-32	3	1
α-helix	40-54	15
α-helix	66-96	31
α-helix	107-129	23
α-helix	142-169	28
α-helix	172-175	4
α-helix	179-187	9
α-helix	195-197	3
α-helix	199-201	3
β-strand	208-211	4	2
β-strand	217-222	6	2
β-strand	228-236	9	2
α-helix	244-273	30
α-helix	280-289	10
α-helix	292-314	23
α-helix	323-340	18
α-helix	347-369	23
α-helix	381-384	4
β-strand	388-391	4	3
α-helix	398-400	3
β-strand	402-405	4	3
β-strand	410-412	3	3
α-helix	421-423	3
α-helix	428-442	15
β-strand	446-450	5	4
α-helix	457-467	11
α-helix	486-496	11
β-strand	503	1	5
α-helix	505-507	3
α-helix	510-527	18
α-helix	528-531	4
β-strand	543-545	3	6
β-strand	550-552	3	6
α-helix	553-554	2
β-strand	560	1	4
β-strand	562	1	5
β-strand	581-585	5	4
α-helix	591-601	11
α-helix	607-621	15
α-helix	626-627	2
α-helix	635-657	23
α-helix	678-690	13
α-helix	699-709	11
α-helix	721-733	13
α-helix	746-759	14
β-strand	766-768	3	7
α-helix	776-790	15
β-strand	793-799	7	7
α-helix	807-810	4
β-strand	811-814	4	8
β-strand	819-822	4	8
α-helix	824-833	10
β-strand	842-848	7	7
α-helix	857-864	8
β-strand	869-872	4	9
β-strand	876-879	4	9
α-helix	880-881	2
β-strand	885-890	6	7
α-helix	898-902	5
β-strand	908	1	7
α-helix	911-913	3
α-helix	916-928	13
α-helix	956-968	13
α-helix	969-971	3
α-helix	978-984	7
α-helix	985-987	3
α-helix	996-1020	25
α-helix	1025-1027	3
α-helix	1028-1047	20
α-helix	1053-1066	14
α-helix	1079-1081	3
β-strand	1082-1085	4	10
β-strand	1089-1092	4	10
α-helix	1093-1096	4
α-helix	1112-1115	4
α-helix	1117-1131	15
β-strand	1136-1139	4	11
α-helix	1146-1156	11
β-strand	1160-1166	7	11
α-helix	1174-1183	10
β-strand	1186	1	12
β-strand	1194-1195	2	13
β-strand	1196	1	12
β-strand	1203-1209	7	11
α-helix	1223-1233	11
β-strand	1236-1238	3	13
β-strand	1245-1248	4	13
β-strand	1251-1257	7	11
α-helix	1267-1269	3
α-helix	1270-1273	4
β-strand	1278-1280	3	11
α-helix	1282-1285	4
α-helix	1286-1300	15
α-helix	1301-1303	3
α-helix	1308-1310	3
α-helix	1311-1327	17
α-helix	1341-1355	15
α-helix	1363-1378	16
α-helix	1385-1402	18
α-helix	1409-1412	4
β-strand	1418-1419	2	14
β-strand	1427-1428	2	14
α-helix	1431-1448	18
α-helix	1458-1472	15
β-strand	1478-1481	4	15
α-helix	1488-1498	11
β-strand	1502-1504	3	15
α-helix	1514-1528	15
α-helix	1530-1532	3
β-strand	1535-1540	6	15
α-helix	1541-1543	3
α-helix	1547-1557	11
α-helix	1568-1585	18
α-helix	1592-1605	14
β-strand	1607-1613	7	15
α-helix	1614	1
α-helix	1616	1
α-helix	1618-1626	9
α-helix	1629-1632	4
β-strand	1635-1638	4	15
α-helix	1640-1642	3
α-helix	1644-1654	11
α-helix	1681-1682	2
α-helix	1684-1708	25
α-helix	1718-1764	47
α-helix	1954-1983	30
α-helix	1986-1997	12
α-helix	2004-2020	17
α-helix	2031-2034	4
α-helix	2038-2046	9
α-helix	2053-2063	11
β-strand	2069-2072	4	16
α-helix	2077-2085	9
β-strand	2092-2095	4	16
α-helix	2101-2111	11
β-strand	2115-2118	4	16
α-helix	2125-2127	3
α-helix	2128-2131	4
β-strand	2136-2138	3	17
β-strand	2141-2144	4	17
β-strand	2151-2152	2	17
β-strand	2159-2163	5	16
α-helix	2172-2176	5
β-strand	2179-2182	4	16
α-helix	2187-2201	15
α-helix	2204-2215	12
α-helix	2219-2238	20
α-helix	2242-2244	3
α-helix	2245-2267	23
α-helix	2269-2299	31
α-helix	2300-2302	3
α-helix	2311-2323	13
α-helix	2326-2328	3
α-helix	2336-2354	19
α-helix	2362-2376	15
α-helix	2384-2391	8
α-helix	2393-2395	3
α-helix	2411-2421	11
α-helix	2430-2434	5
α-helix	2438-2442	5
α-helix	2464-2477	14
α-helix	2480-2482	3
α-helix	2483-2495	13
α-helix	2501-2504	4
α-helix	2506-2507	2
α-helix	2509-2511	3
α-helix	2512-2516	5
β-strand	2523-2527	5	18
α-helix	2534-2544	11
β-strand	2548-2551	4	18
α-helix	2556-2569	14
β-strand	2575-2578	4	18
α-helix	2585-2595	11
β-strand	2606-2611	6	18
α-helix	2618-2623	6
β-strand	2626-2629	4	18
α-helix	2631-2633	3
α-helix	2635-2645	11
α-helix	2648-2652	5
α-helix	2658-2674	17
α-helix	2675-2677	3
α-helix	2691-2708	18
α-helix	2722-2728	7
α-helix	2729-2733	5
α-helix	2741-2754	14
α-helix	2757-2760	4
β-strand	2765-2767	3	19
β-strand	2776-2777	2	19
α-helix	2778-2780	3
α-helix	2784-2792	9
α-helix	2800-2803	4
α-helix	2809-2827	19
α-helix	2858-2872	15
α-helix	2890-2920	31
α-helix	2928-2938	11
α-helix	2944-2946	3
α-helix	2957-2980	24
α-helix	2985-2988	4
β-strand	2990-2992	3	20
α-helix	2993-2995	3
α-helix	2999-3013	15
α-helix	3018-3020	3
β-strand	3021-3027	7	20
β-strand	3039-3043	5	20
β-strand	3046-3048	3	21
β-strand	3050-3052	3	21
β-strand	3056-3059	4	21
β-strand	3065-3066	2	21
β-strand	3070-3076	7	20
α-helix	3081-3083	3
β-strand	3086-3092	7	21
β-strand	3100-3108	9	21
α-helix	3114-3120	7
β-strand	3123-3125	3	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase	A	protein	3130	Homo sapiens, Thermus thermophilus	Q14204, Q5SJX7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8FCY_1 Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase (chains A)
GSALEEFLKQIREVWNTYELDLVNYQNKCRLIRGWDDLFNKVKEHINSVSAMKLSPYYKV
FEEDALSWEDKLNRIMALFDVWIDVQRRWVYLEGIFTGSADIKHLLPVETQRFQSISTEF
LALMKKVSKSPLVMDVLNIQGVQRSLERLADLLGKIQKALGEYLERERSSFPRFYFVGDE
DLLEIIGNSKNVAKLQKHFKKMFAGVSSIILNEDNSVVLGISSREGEEVMFKTPVSITEH
PKINEWLTLVEKEMRVTLAKLLAESVTEVEIFGKATSIDPNTYITWIDKYQAQLVVLSAQ
IAWSENVETALSSMGGGGDAAPLHSVLSNVEVTLNVLADSVLMEQPPLRRRKLEHLITEL
VHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPKQTDVLQQLSIQMANAKFNYGFEYLGV
QDKLVQTPLTDRCYLTMTQALEARLGGSPFGPAGTGKTESVKALGHQLGRFVLVFNCDET
FDFQAMGRIFVGLCQVGAWGCFDEFNRLEERMLSAVSQQVQCIQEALREHSNPNYDKTSA
PITCELLNKQVKVSPDMAIFITMNPGYAGRSNLPDNLKKLFRSLAMTKPDRQLIAQVMLY
SQGFRTAEVLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLVSAGNVKRERIQKIKREK
EERGEAVDEGEIAENLPEQEILIQSVCETMVPKLVAEDIPLLFSLLSDVFPGVQYHRGEM
TALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINHGLMMVGPSGSGKSMAWR
VLLKALERLEGVEGVAHIIDPKAISKDHLYGTLDPNTREWTDGLFTHVLRKIIDSVRGEL
QKRQWIVFDGDVDPEWVENLNSVLDDNKLLTLPNGERLSLPPNVRIMFEVQDLKYATLAT
VSRCGMVWFSEDVLSTDMIFNNFLARLRSIPLDEGEDEAQRRRKGKEDEGEEAASPMLQI
QRDAATIMQPYFTSNGLVTKALEHAFQLEHIMDLTRLRCLGSLFSMLHQACRNVAQYNAN
HPDFPMQIEQLERYIQRYLVYAILWSLSGDSRLKMRAELGEYIRRITTVPLPTAPNIPII
DYEVSISGEWSPWQAKVPQIEVETHKVAAPDVVVPTLDTVRHEALLYTWLAEHKPLVLCG
PPGSGKTMTLFSALRALPDMEVVGLNFSSATTPELLLKTFDHYCEYRRTPNGVVLAPVQL
GKWLVLFCDEINLPDMDKYGTQRVISFIRQMVEHGGFYRTSDQTWVKLERIQFVGACNPP
TDPGRKPLSHRFLRHVPVVYVDYPGPASLTQIYGTFNRAMLRLIPSLRTYAEPLTAAMVE
FYTMSQERFTQDTQPHYIYSPREMTRWVRGIFEALRPLETLPVEGLIRIWAHEALRLFQD
RLVEDEERRWTDENIDTVALKHFPNIDREKAMSRPILYSNWLSKDYIPVDQEELRDYVKA
RLKVFYEEELDVPLVLFNEVLDHVLRIDRIFRQPQGHLLLIGVSGAGKTTLSRFVAWMNG
LSVYQIKVHRKYTGEDFDEDLRTVLRRSGCKNEKIAFIMDESNVLDSGFLERMNTLLANG
EVPGLFEGDEYATLMTQCKEGAQKEGLMLDSHEELYKWFTSQVIRNLHVVFTMNPSSEGL
KDRAATSPALFNRCVLNWFGDWSTEALYQVGKEFTSKMDLEKPNYIVPDYMPVVYDKLPQ
PPSHREAIVNSCVFVHQTLHQANARLAKRGGRTMAITPRHYLDFINHYANLFHEKRSELE
EQQMHLNVGLRKIKETVDQVEELRRDLRIKSQELEVKNAAANDKLKKMVKDQQEAEKKKV
MSQEIQEQLHKQQEVIADKQMSVKEDLLALDQEVQELKKRLQEVQTERNQVAKRVPKAPP
EEKEALIARGRALGEEAKRLEEALREKEAQLEALRNELQKLEDDAKDNQQKANEVEQMIR
DLEASIARYKEEYAVLISEAQAIKADLAAVEAKVNRSTALLKSLSAERERWEKTSETFKN
QMSTIAGDCLLSAAFIAYAGYFDQQMRQNLFTTWSHHLQQANIQFRTDIARTEYLSNADE
RLRWQASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATEFIMNEYKDRKITRTSFLDDA
FRKNLESALRFGNPLLVQDVESYDPVLNPVLNREVRRTGGRVLITLGDQDIDLSPSFVIF
LSTRDPTVEFPPDLCSRVTFVNFTVTRSSLQSQCLNEVLKAERPDVDEKRSDLLKLQGEF
QLRLRQLEKSLLQALNEVKGRILDDDTIITTLENLKREAAEVTRKVEETDIVMQEVETVS
QQYLPLSTACSSIYFTMESLKQIHFLYQYSLQFFLDIYHNVLYENPNLKGVTDHTQRLSI
ITKDLFQVAFNRVARGMLHQDHITFAMLLARIKLKGTVGEPTYDAEFQHFLRGNEIVLSA
GSTPRIQGLTVEQAEAVVRLSCLPAFKDLIAKVQADEQFGIWLDSSSPEQTVPYLWSEET
PATPIGQAIHRLLLIQAFRPDRLLAMAHMFVSTNLGESFMSIMEQPLDLTHIVGTEVKPN
TPVLMCSVPGYDASGHVEDLAAEQNTQITSIAIGSAEGFNQADKAINTAVKSGRWVMLKN
VHLAPGWLMQLEKKLHSLQPHACFRLFLTMEINPKVPVNLLRAGRIFVFEPPPGVKANML
RTFSSIPVSRICKSPNERARLYFLLAWFHAIIQERLRYAPLGWSKKYEFGESDLRSACDT
VDTWLDDTAKGRQNISPDKIPWSALKTLMAQSIYGGRVDNEFDQRLLNTFLERLFTTRSF
DSEFKLACKVDGHKDIQMPDGIRREEFVQWVELLPDTQTPSWLGLPNNAERVLLTTQGVD
MISKMLKMQMLEDEDDLAYAETEKKTRTDSTSDGRPAWMRTLHTTASNWLHLIPQTLSHL
KRTVENIKDPLFRFFEREVKMGAKLLQDVRQDLADVVQVCEGKKKQTNYLRTLINELVKG
ILPRSWSHYTVPAGMTVIQWVSDFSERIKQLQNISLAAASGGAKELKNIHVCLGGLFVPE
AYITATRQYVAQANSWSLEELCLEVNVTTSQGATLDACSFGVTGLKLQGATCNNNKLSLS
NAISTALPLTQLRWVKQTNTEKKASVVTLPVYLNFTRADLIFTVDFEIATKEDPRSFYER
GVAVLCTEEF

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

Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport. Ton, W.D., Wang, Y., Chai, P. et al. Nat Struct Mol Biol (2023) 30:1365-1379. DOI 10.1038/s41594-023-01010-x · 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

Browse structure collections

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