8FDU: PDB entry 8FDU

Engineered human dynein motor domain in the microtubule-unbound state with LIS1 complex in the buffer containing ATP-Vi (local refined on AAA3-AAA5 and LIS1). Determined by electron microscopy at 3.3 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Thermus thermophilus
Chains: 3
Atoms: 13,193
Mol. weight: 491.16 kDa
Ligands: ADP
Released: 21 Jun 2023

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

Secondary structure: helices and β-sheets

8FDU contains 54 α-helices and 83 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: 48 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	1117-1131	15
β-strand	1136-1139	4	1
α-helix	1146-1156	11
β-strand	1160-1166	7	1
α-helix	1173-1183	11
β-strand	1186	1	2
β-strand	1193-1195	3	3
β-strand	1196	1	2
β-strand	1203-1209	7	1
β-strand	1217	1	4
β-strand	1221	1	4
α-helix	1223-1233	11
β-strand	1236-1238	3	3
β-strand	1245-1248	4	3
β-strand	1252-1257	6	1
α-helix	1267-1269	3
α-helix	1270-1273	4
β-strand	1278-1280	3	1
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	5
β-strand	1427-1428	2	5
α-helix	1431-1448	18
α-helix	1458-1472	15
β-strand	1478-1482	5	6
α-helix	1488-1498	11
β-strand	1504-1505	2	6
α-helix	1514-1528	15
β-strand	1536-1540	5	6
α-helix	1547-1559	13
α-helix	1569-1585	17
α-helix	1592-1605	14
β-strand	1608-1613	6	6
α-helix	1619-1626	8
α-helix	1629-1632	4
β-strand	1635-1640	6	6
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	7
α-helix	2073-2081	9
α-helix	2083-2085	3
β-strand	2088-2091	4	7
α-helix	2097-2107	11
β-strand	2111-2114	4	7
α-helix	2116-2118	3
α-helix	2121-2123	3
α-helix	2124-2128	5
β-strand	2132-2133	2	8
β-strand	2138-2142	5	8
β-strand	2145-2149	5	8
β-strand	2155-2159	5	7
α-helix	2168-2171	4
β-strand	2175-2178	4	7
α-helix	2183-2198	16
α-helix	2200-2233	34
α-helix	2241-2263	23
α-helix	2264-2268	5
α-helix	2269-2277	9

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	97-105	9	9
β-strand	112-117	6	10
β-strand	124-128	5	10
β-strand	133-137	5	10
β-strand	142-147	6	10
β-strand	154-159	6	11
β-strand	165-170	6	11
β-strand	174-179	6	11
β-strand	184-190	7	11
β-strand	196-201	6	12
β-strand	207-212	6	12
β-strand	216-221	6	12
β-strand	229-232	4	12
β-strand	238-243	6	13
β-strand	249-254	6	13
β-strand	259-263	5	13
β-strand	269-273	5	13
β-strand	280-285	6	14
α-helix	288-298	11
α-helix	300-302	3
β-strand	311-316	6	14
β-strand	320-325	6	14
β-strand	330-336	7	14
β-strand	342-347	6	15
β-strand	354-358	5	15
β-strand	363-366	4	15
β-strand	374-377	4	15
β-strand	384-389	6	9
β-strand	395-400	6	9
β-strand	405-410	6	9

Chain C: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	97-106	10	16
β-strand	112-117	6	17
β-strand	124-128	5	17
β-strand	133-137	5	17
β-strand	142-145	4	17
β-strand	154-159	6	18
β-strand	165-170	6	18
β-strand	175-179	5	18
β-strand	184-189	6	18
β-strand	196-201	6	19
β-strand	207-212	6	19
β-strand	216-221	6	19
β-strand	227-232	6	19
β-strand	238-243	6	20
β-strand	249-254	6	20
β-strand	259-263	5	20
β-strand	269-273	5	20
β-strand	280-285	6	21
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	21
β-strand	320-325	6	21
β-strand	330-336	7	21
β-strand	342-347	6	22
β-strand	354-358	5	22
β-strand	363-366	4	22
β-strand	374-377	4	22
β-strand	387-389	3	16
β-strand	395-398	4	16
β-strand	404-410	7	16

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,Platelet-activating factor…	B, C	protein	598	Homo sapiens	P43034 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8FDU_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

>8FDU_2 Platelet-activating factor acetylhydrolase IB subunit beta,Platelet-activating factor acetylhydrolase IB subunit beta,human LIS1 protein with a SNAP tag (chains B, C)
GSVLSQRQRDELNRAIADYLRSNGYEEAYSVFKKEAELDVNEELDKKYAGLLEKKWTSVI
RLQKKVMELESKLNEAKEEFTSGGPLGQKRDPKEWIPRPPEKYALSGHRSPVTRVIFHPV
FSVMVSASEDATIKVWDYETGDFERTLKGHTDSVQDISFDHSGKLLASCSADMTIKLWDF
QGFECIRTMHGHDHNVSSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRM
VRPNQDGTLIASCSNDQTVRVWVVATKECKAELREHEHVVECISWAPESSYSSISEATGS
ETKKSGKPGPFLLSGSRDKTIKMWDVSTGMCLMTLVGHDNWVRGVLFHSGGKFILSCADD
KTLRVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGSVDQTVKVWECRGAGAGADKD
CEMKRTTLDSPLGKLELSGCEQGLHRIIFLGKGTSAADAVEVPAPAAVLGGPEPLMQATA
WLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYSHLAALAGNP
AATAAVKTALSGNPVPILIPCHRVVQGDLDVGGYEGGLAVKEWLLAHEGHRLGKPGLG

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2

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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