8FDT: PDB entry 8FDT

Engineered human dynein motor domain in the microtubule-unbound state with LIS1 complex in the buffer containing ATP-Vi. Determined by electron microscopy at 3.2 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Thermus thermophilus
Chains: 3
Atoms: 27,096
Mol. weight: 492.21 kDa
Ligands: ATP, ADP, VO4
Released: 21 Jun 2023

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

Secondary structure: helices and β-sheets

8FDT contains 147 α-helices and 128 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: 141 helices, 72 β-strands

Element	Residues	Length	Sheet
α-helix	89-95	7
α-helix	101-104	4
α-helix	108-113	6
α-helix	153-170	18
α-helix	172-175	4
α-helix	179-187	9
α-helix	193-195	3
α-helix	199-202	4
β-strand	206-211	6	1
β-strand	217-223	7	1
β-strand	228-236	9	1
α-helix	243-273	31
α-helix	280-289	10
α-helix	292-314	23
α-helix	323-342	20
α-helix	347-373	27
α-helix	381-384	4
β-strand	388	1	2
β-strand	391	1	3
β-strand	402	1	3
β-strand	405-406	2	2
β-strand	409-410	2	2
α-helix	428-442	15
β-strand	446-450	5	4
α-helix	458-467	10
β-strand	472-476	5	4
α-helix	483-496	14
β-strand	499-503	5	4
α-helix	505-507	3
α-helix	510-531	22
β-strand	542-545	4	5
β-strand	550-553	4	5
β-strand	558-561	4	4
β-strand	563	1	4
α-helix	571-574	4
α-helix	575-578	4
β-strand	581-585	5	4
α-helix	591-602	12
α-helix	607-624	18
α-helix	626-627	2
α-helix	635-658	24
α-helix	678-689	12
α-helix	691-693	3
α-helix	699-709	11
α-helix	721-733	13
α-helix	746-761	16
β-strand	764-768	5	6
α-helix	775-789	15
β-strand	796-799	4	6
α-helix	806-810	5
β-strand	811-813	3	7
β-strand	820-822	3	7
α-helix	824-833	10
α-helix	839-841	3
β-strand	844-848	5	6
α-helix	857-860	4
β-strand	869-871	3	8
β-strand	877-879	3	8
β-strand	884-890	7	6
α-helix	898-902	5
β-strand	905-908	4	6
α-helix	916-927	12
α-helix	956-968	13
α-helix	969-972	4
α-helix	977-987	11
α-helix	996-1020	25
α-helix	1028-1047	20
α-helix	1053-1065	13
α-helix	1079-1081	3
β-strand	1082	1	9
β-strand	1092	1	9
α-helix	1117-1131	15
β-strand	1136-1139	4	10
α-helix	1146-1156	11
β-strand	1160-1166	7	10
α-helix	1173-1183	11
β-strand	1186	1	11
β-strand	1193-1195	3	12
β-strand	1196	1	11
β-strand	1203-1209	7	10
β-strand	1216	1	13
β-strand	1222	1	13
α-helix	1223-1233	11
β-strand	1236-1238	3	12
β-strand	1245-1248	4	12
β-strand	1252-1257	6	10
α-helix	1267-1269	3
α-helix	1270-1273	4
β-strand	1278-1280	3	10
α-helix	1282-1285	4
α-helix	1286-1300	15
α-helix	1301-1303	3
α-helix	1308-1310	3
α-helix	1311-1328	18
α-helix	1341-1354	14
α-helix	1363-1378	16
α-helix	1385-1402	18
α-helix	1408-1411	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	1478-1482	5	15
α-helix	1488-1498	11
β-strand	1504-1505	2	15
α-helix	1514-1528	15
β-strand	1536-1540	5	15
α-helix	1547-1559	13
α-helix	1569-1585	17
α-helix	1592-1605	14
β-strand	1608-1613	6	15
α-helix	1619-1626	8
α-helix	1629-1632	4
β-strand	1635-1640	6	15
α-helix	1644-1654	11
α-helix	1666-1668	3
α-helix	1684-1708	25
α-helix	1714-1716	3
α-helix	1718-1764	47
α-helix	1951-1979	29
α-helix	1981-1993	13
α-helix	2000-2016	17
α-helix	2027-2031	5
α-helix	2034-2042	9
α-helix	2049-2059	11
α-helix	2064	1
β-strand	2065-2068	4	16
α-helix	2073-2081	9
α-helix	2083-2085	3
β-strand	2088-2091	4	16
α-helix	2097-2107	11
β-strand	2111-2114	4	16
α-helix	2116-2118	3
α-helix	2121-2123	3
α-helix	2124-2128	5
β-strand	2132-2133	2	17
β-strand	2138-2142	5	17
β-strand	2145-2149	5	17
β-strand	2155-2159	5	16
α-helix	2168-2171	4
β-strand	2175-2178	4	16
α-helix	2180-2182	3
α-helix	2183-2198	16
α-helix	2200-2233	34
α-helix	2241-2263	23
α-helix	2264-2268	5
α-helix	2269-2295	27
α-helix	2296-2298	3
α-helix	2307-2318	12
α-helix	2330-2350	21
α-helix	2358-2371	14
α-helix	2380-2387	8
α-helix	2407-2416	10
α-helix	2420-2422	3
α-helix	2425-2430	6
α-helix	2434-2439	6
α-helix	2457-2459	3
α-helix	2460-2474	15
α-helix	2476-2478	3
α-helix	2479-2491	13
α-helix	2498-2500	3
α-helix	2502-2503	2
α-helix	2505-2507	3
α-helix	2508-2512	5
α-helix	2518	1
β-strand	2519-2523	5	18
α-helix	2530-2539	10
β-strand	2544-2548	5	18
α-helix	2554-2565	12
β-strand	2571-2575	5	18
α-helix	2581-2591	11
α-helix	2596-2597	2
β-strand	2602-2607	6	18
α-helix	2614-2619	6
β-strand	2621-2625	5	18
α-helix	2627-2628	2
α-helix	2630-2641	12
α-helix	2653-2671	19
α-helix	2672-2674	3
α-helix	2687-2704	18
α-helix	2713-2715	3
α-helix	2718-2724	7
α-helix	2725-2729	5
α-helix	2731-2733	3
α-helix	2737-2750	14
α-helix	2753-2756	4
β-strand	2761	1	19
α-helix	2772	1
β-strand	2773	1	19
α-helix	2774-2775	2
α-helix	2780-2788	9
α-helix	2796-2798	3
α-helix	2807-2824	18
α-helix	2854-2868	15
α-helix	2870-2874	5
α-helix	2886-2916	31
α-helix	2924-2934	11
α-helix	2937-2939	3
α-helix	2953-2976	24
β-strand	2986-2988	3	20
α-helix	2995-3009	15
β-strand	3018-3023	6	20
β-strand	3037-3039	3	20
β-strand	3041-3043	3	21
β-strand	3047-3048	2	21
β-strand	3052-3054	3	21
β-strand	3061-3063	3	21
β-strand	3066-3071	6	20
α-helix	3077-3079	3
β-strand	3082-3088	7	21
β-strand	3096-3104	9	21
α-helix	3110-3115	6
β-strand	3120-3121	2	21

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	97-105	9	22
β-strand	112-117	6	23
β-strand	124-128	5	23
β-strand	133-137	5	23
β-strand	142-147	6	23
β-strand	154-159	6	24
β-strand	165-170	6	24
β-strand	174-179	6	24
β-strand	184-190	7	24
β-strand	196-201	6	25
β-strand	207-212	6	25
β-strand	216-221	6	25
β-strand	229-232	4	25
β-strand	238-243	6	26
β-strand	249-254	6	26
β-strand	259-263	5	26
β-strand	269-273	5	26
β-strand	280-285	6	27
α-helix	288-298	11
α-helix	300-302	3
β-strand	311-316	6	27
β-strand	320-325	6	27
β-strand	330-336	7	27
β-strand	342-347	6	28
β-strand	354-358	5	28
β-strand	363-366	4	28
β-strand	374-377	4	28
β-strand	384-389	6	22
β-strand	395-400	6	22
β-strand	405-410	6	22

Chain C: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	97-105	9	29
β-strand	112-117	6	30
β-strand	124-128	5	30
β-strand	133-137	5	30
β-strand	142-145	4	30
β-strand	154-159	6	31
β-strand	165-170	6	31
β-strand	175-179	5	31
β-strand	184-189	6	31
β-strand	196-201	6	32
β-strand	207-212	6	32
β-strand	216-221	6	32
β-strand	227-232	6	32
β-strand	238-243	6	33
β-strand	249-254	6	33
β-strand	259-263	5	33
β-strand	269-273	5	33
β-strand	280-285	6	34
α-helix	286-287	2
α-helix	288-290	3
α-helix	291-298	8
α-helix	300-302	3
β-strand	311-316	6	34
β-strand	320-325	6	34
β-strand	330-336	7	34
β-strand	342-347	6	35
β-strand	354-358	5	35
β-strand	363-366	4	35
β-strand	374-377	4	35
β-strand	387-389	3	29
β-strand	395-398	4	29
β-strand	405-410	6	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase	A	protein	3126	Homo sapiens, Thermus thermophilus	Q14204, Q5SJX7 (AlphaFold model)
Platelet-activating factor acetylhydrolase IB subunit beta	B, C	protein	598	Homo sapiens	P43034 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8FDT_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
MSQEIQEQLHKQQEVIADKQMSLLALDQEVQELKKRLQEVQTERNQVAKRVPKAPPEEKE
ALIARGRALGEEAKRLEEALREKEAQLEALRNELQKLEDDAKDNQQKANEVEQMIRDLEA
SIARYKEEYAVLISEAQAIKADLAAVEAKVNRSTALLKSLSAERERWEKTSETFKNQMST
IAGDCLLSAAFIAYAGYFDQQMRQNLFTTWSHHLQQANIQFRTDIARTEYLSNADERLRW
QASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATEFIMNEYKDRKITRTSFLDDAFRKN
LESALRFGNPLLVQDVESYDPVLNPVLNREVRRTGGRVLITLGDQDIDLSPSFVIFLSTR
DPTVEFPPDLCSRVTFVNFTVTRSSLQSQCLNEVLKAERPDVDEKRSDLLKLQGEFQLRL
RQLEKSLLQALNEVKGRILDDDTIITTLENLKREAAEVTRKVEETDIVMQEVETVSQQYL
PLSTACSSIYFTMESLKQIHFLYQYSLQFFLDIYHNVLYENPNLKGVTDHTQRLSIITKD
LFQVAFNRVARGMLHQDHITFAMLLARIKLKGTVGEPTYDAEFQHFLRGNEIVLSAGSTP
RIQGLTVEQAEAVVRLSCLPAFKDLIAKVQADEQFGIWLDSSSPEQTVPYLWSEETPATP
IGQAIHRLLLIQAFRPDRLLAMAHMFVSTNLGESFMSIMEQPLDLTHIVGTEVKPNTPVL
MCSVPGYDASGHVEDLAAEQNTQITSIAIGSAEGFNQADKAINTAVKSGRWVMLKNVHLA
PGWLMQLEKKLHSLQPHACFRLFLTMEINPKVPVNLLRAGRIFVFEPPPGVKANMLRTFS
SIPVSRICKSPNERARLYFLLAWFHAIIQERLRYAPLGWSKKYEFGESDLRSACDTVDTW
LDDTAKGRQNISPDKIPWSALKTLMAQSIYGGRVDNEFDQRLLNTFLERLFTTRSFDSEF
KLACKVDGHKDIQMPDGIRREEFVQWVELLPDTQTPSWLGLPNNAERVLLTTQGVDMISK
MLKMQMLEDEDDLAYAETEKKTRTDSTSDGRPAWMRTLHTTASNWLHLIPQTLSHLKRTV
ENIKDPLFRFFEREVKMGAKLLQDVRQDLADVVQVCEGKKKQTNYLRTLINELVKGILPR
SWSHYTVPAGMTVIQWVSDFSERIKQLQNISLAAASGGAKELKNIHVCLGGLFVPEAYIT
ATRQYVAQANSWSLEELCLEVNVTTSQGATLDACSFGVTGLKLQGATCNNNKLSLSNAIS
TALPLTQLRWVKQTNTEKKASVVTLPVYLNFTRADLIFTVDFEIATKEDPRSFYERGVAV
LCTEEF

Sequence of entity 2 (B, C), FASTA

>8FDT_2 Platelet-activating factor acetylhydrolase IB subunit beta (chains B, C)
GSVLSQRQRDELNRAIADYLRSNGYEEAYSVFKKEAELDVNEELDKKYAGLLEKKWTSVI
RLQKKVMELESKLNEAKEEFTSGGPLGQKRDPKEWIPRPPEKYALSGHRSPVTRVIFHPV
FSVMVSASEDATIKVWDYETGDFERTLKGHTDSVQDISFDHSGKLLASCSADMTIKLWDF
QGFECIRTMHGHDHNVSSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRM
VRPNQDGTLIASCSNDQTVRVWVVATKECKAELREHEHVVECISWAPESSYSSISEATGS
ETKKSGKPGPFLLSGSRDKTIKMWDVSTGMCLMTLVGHDNWVRGVLFHSGGKFILSCADD
KTLRVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGSVDQTVKVWECRGAGAGADKD
CEMKRTTLDSPLGKLELSGCEQGLHRIIFLGKGTSAADAVEVPAPAAVLGGPEPLMQATA
WLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYSHLAALAGNP
AATAAVKTALSGNPVPILIPCHRVVQGDLDVGGYEGGLAVKEWLLAHEGHRLGKPGLG

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
VO4	Vanadate ion	O4 V	1

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

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