8FD6: PDB entry 8FD6

Engineered human dynein motor domain in the microtubule-unbound state in the buffer containing ATP-Vi. Determined by electron microscopy at 2.9 Å resolution. Released 21 Jun 2023.

Method
Electron microscopy
Resolution
2.9 Å
Organisms
Homo sapiens, Thermus thermophilus
Chains
1
Atoms
22,170
Mol. weight
359.39 kDa
Ligands
ATP, ADP, VO4, MG
Released
21 Jun 2023

Explore 8FD6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FD6 contains 142 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: 142 helices, 69 β-strands

ElementResiduesLengthSheet
α-helix89-968
α-helix101-1044
α-helix108-1136
α-helix153-17018
α-helix172-1765
α-helix179-1879
α-helix192-1976
α-helix199-2024
β-strand206-21161
β-strand217-22371
β-strand228-23691
α-helix243-27331
α-helix280-28910
α-helix292-31322
α-helix323-34220
α-helix347-37327
α-helix381-3844
β-strand388-39142
β-strand402-40542
β-strand411-41222
α-helix423-4253
α-helix428-44114
α-helix442-4443
β-strand446-45053
α-helix457-46711
β-strand472-47653
α-helix483-49614
β-strand499-50353
α-helix505-5073
α-helix510-52718
β-strand543-54534
β-strand550-55234
α-helix553-5542
β-strand558-56363
α-helix575-5784
β-strand581-58553
α-helix591-60212
α-helix607-62418
α-helix626-6272
α-helix635-65824
α-helix678-68912
α-helix696-6983
α-helix699-70911
α-helix721-73313
α-helix746-76116
β-strand764-76855
α-helix775-79016
α-helix792-7932
β-strand794-79965
α-helix806-8105
β-strand811-81336
β-strand820-82236
α-helix824-83310
α-helix839-8413
β-strand843-84975
α-helix858-8603
β-strand869-87137
β-strand877-87937
α-helix880-8812
β-strand884-89075
α-helix898-9036
β-strand905-90845
α-helix916-92813
α-helix956-96813
α-helix969-9713
α-helix977-9859
α-helix996-102025
α-helix1028-104821
α-helix1053-106614
α-helix1079-10813
β-strand1082-108438
β-strand1090-109238
α-helix1093-10964
α-helix1117-113115
β-strand1136-113949
α-helix1146-115611
β-strand1160-116679
α-helix1173-118311
β-strand1186-1188310
β-strand1193-1196410
β-strand1203-120979
α-helix1215-12162
α-helix1223-123311
β-strand1236-1238310
β-strand1245-1248410
β-strand1251-125779
α-helix1267-12693
α-helix1270-12734
β-strand1278-128039
α-helix1282-12843
α-helix1286-130015
α-helix1308-13103
α-helix1311-132818
α-helix1341-135515
α-helix1363-137816
α-helix1385-140218
α-helix1408-14114
β-strand1418-1419211
β-strand1427-1428211
α-helix1431-144818
α-helix1458-147215
β-strand1477-1482612
α-helix1488-149912
β-strand1502-1505412
α-helix1514-152916
β-strand1535-1540612
α-helix1547-155913
α-helix1569-158517
α-helix1592-160514
β-strand1608-1613612
α-helix1620-16267
α-helix1628-16303
β-strand1634-1640712
α-helix1642-16432
α-helix1644-165512
α-helix1684-170825
α-helix1718-176447
α-helix1951-197929
α-helix1981-199414
α-helix2000-201617
α-helix2027-20304
α-helix2034-20429
α-helix2049-205911
α-helix20641
β-strand2065-2068413
α-helix2073-20819
β-strand2088-2091413
α-helix2097-210711
β-strand2111-2114413
α-helix2116-21183
α-helix2121-21233
α-helix2124-21285
β-strand2132-2134314
β-strand2137-2142614
β-strand2145-2148414
β-strand2155-2159513
α-helix2168-21714
β-strand2175-2178413
α-helix2183-219816
α-helix2200-223334
α-helix2241-226323
α-helix2264-22685
α-helix2269-22768
α-helix2280-229516
α-helix2307-231913
α-helix2322-23243
α-helix2330-235021
α-helix2355-23573
α-helix2358-237114
α-helix2380-23889
α-helix2407-241610
α-helix2425-24306
α-helix2434-24396
α-helix2444-24463
α-helix2460-247415
α-helix2476-24783
α-helix2479-249012
α-helix2502-25032
α-helix2505-25117
β-strand2519-2523515
α-helix2530-253910
β-strand2544-2548515
α-helix2554-256613
β-strand2571-2575515
α-helix2581-259111
α-helix2596-25972
β-strand2601-2607715
α-helix2614-26196
β-strand2621-2625515
α-helix2627-26282
α-helix2630-264112
α-helix2653-267018
α-helix2672-26743
α-helix2687-270418
α-helix2718-27225
α-helix27241
α-helix2725-27295
α-helix2737-275014
α-helix2753-27553
β-strand2761-2763316
β-strand2772-2773216
α-helix2774-27752
α-helix2780-27889
α-helix2796-27994
α-helix2803-28053
α-helix2807-282418
α-helix2854-286815
α-helix2872-28743
α-helix2886-291631
α-helix2924-293411
β-strand2937117
α-helix2938-29392
β-strand2952117
α-helix2953-297624
α-helix29861
β-strand2987-2988218
α-helix2995-300915
β-strand3018-3023618
β-strand3035-3039518
β-strand3041-3043319
β-strand3046120
β-strand3052-3053219
β-strand3055120
β-strand3061-3063319
β-strand3066-3071618
α-helix3077-30793
β-strand3082-3088719
β-strand3096-3104919
α-helix31051
α-helix3110-31156
β-strand3120-3121219

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligaseAprotein3126Homo sapiens, Thermus thermophilusQ14204, Q5SJX7 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8FD6_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

Ligands and cofactors

IDNameFormulaCopies
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P23
VO4Vanadate ionO4 V1
MGMagnesium ionMg1

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:

Browse structure collections

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