8PTK: Composite structure of Dynein-Dynactin-JIP3-LIS1

Composite structure of Dynein-Dynactin-JIP3-LIS1. Determined by electron microscopy at 10.0 Å resolution. Released 27 Mar 2024.

Method
Electron microscopy
Resolution
10.0 Å
Organisms
Homo sapiens, Sus scrofa
Chains
53
Atoms
161,538
Mol. weight
4180.97 kDa
Ligands
ANP, MG, ZN, ATP
Released
27 Mar 2024

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

Secondary structure: helices and β-sheets

8PTK contains 1,365 α-helices and 1,056 β-strands across 53 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 1: 7 helices, 32 β-strands

ElementResiduesLengthSheet
α-helix5-2117
α-helix25-3410
α-helix50-567
α-helix58-7922
α-helix91-933
β-strand9611
β-strand102-10542
β-strand111-11663
β-strand123-12753
β-strand132-13543
β-strand142-14653
β-strand153-15864
β-strand164-16964
β-strand173-17864
β-strand183-18974
β-strand19515
β-strand199-20026
β-strand206-21056
β-strand21115
β-strand215-22066
β-strand226-23166
β-strand237-24267
β-strand248-25367
β-strand258-26257
β-strand268-27257
β-strand281-28448
α-helix285-2862
α-helix287-29610
β-strand310-31458
β-strand319-32468
β-strand329-33578
β-strand341-34669
β-strand352-35769
β-strand362-36659
β-strand371-37669
β-strand383-38862
β-strand394-39962
β-strand403-40862
β-strand40911
Chain 2: 8 helices, 30 β-strands
ElementResiduesLengthSheet
α-helix5-2016
α-helix25-3511
α-helix41-444
α-helix50-7930
α-helix91-933
β-strand96112
β-strand102-105413
β-strand111-116614
β-strand123-127514
β-strand132-136514
β-strand141-146614
β-strand155-158415
β-strand164-168515
β-strand174-178515
β-strand184-188515
β-strand195-200616
β-strand206-211616
β-strand215-220616
β-strand226-231616
β-strand237-242617
β-strand248-253617
β-strand258-262517
β-strand268-272517
β-strand279-284618
α-helix285-2862
α-helix287-2893
α-helix290-2978
β-strand310-315618
β-strand319-324618
β-strand329-335718
β-strand341-346619
β-strand352-357619
β-strand361-366619
β-strand371-377719
β-strand383-388613
β-strand394-399613
β-strand403-408613
β-strand409112
Chain 3: 3 helices, 32 β-strands
ElementResiduesLengthSheet
α-helix91-933
β-strand96128
β-strand102-105429
β-strand111-116630
β-strand123-127530
β-strand132-135430
β-strand142-146530
β-strand153-158631
β-strand164-169631
β-strand173-178631
β-strand183-189731
β-strand195132
β-strand199-200233
β-strand206-210533
β-strand211132
β-strand215-220633
β-strand226-231633
β-strand237-242634
β-strand248-253634
β-strand258-262534
β-strand268-272534
β-strand279-284635
α-helix285-2862
α-helix288-2969
β-strand310-315635
β-strand319-324635
β-strand329-335735
β-strand341-346636
β-strand352-357636
β-strand362-366536
β-strand371-376636
β-strand383-388629
β-strand394-399629
β-strand403-408629
β-strand409128
Chain 4: 3 helices, 30 β-strands
ElementResiduesLengthSheet
α-helix91-933
β-strand96138
β-strand102-105439
β-strand111-116640
β-strand123-127540
β-strand132-135440
β-strand142-146540
β-strand155-158441
β-strand164-168541
β-strand173-178641
β-strand184-189641
β-strand195-200642
β-strand206-211642
β-strand215-220642
β-strand226-231642
β-strand237-242643
β-strand248-253643
β-strand258-262543
β-strand268-272543
β-strand279-284644
α-helix285-2862
α-helix290-2978
β-strand310-315644
β-strand319-324644
β-strand329-335744
β-strand341-346645
β-strand352-357645
β-strand361-366645
β-strand371-377745
β-strand383-388639
β-strand394-399639
β-strand403-408639
β-strand409138
Chain a: 2 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand7-12637
α-helix15-3117
α-helix35-4915
β-strand54-681537
β-strand73-78637
β-strand81-87737
Chain A: 21 helices, 23 β-strands
ElementResiduesLengthSheet
α-helix10-112
β-strand12-15446
β-strand20-21247
β-strand22-25446
β-strand35-36247
β-strand39-42448
β-strand45-46249
β-strand57148
α-helix60-645
β-strand69-72448
β-strand75-76250
β-strand79-80250
α-helix83-9311
β-strand108-112546
α-helix118-1269
α-helix127-1315
β-strand137-141546
α-helix142-1498
β-strand155-160651
β-strand165-171751
β-strand174-175251
α-helix1761
β-strand181-183351
α-helix187-20014
α-helix211-22010
β-strand223152
α-helix228-2325
α-helix235-2373
β-strand240-242353
β-strand248-250353
α-helix254-2574
α-helix258-2614
α-helix275-28410
α-helix291-2966
β-strand298-301451
β-strand308152
α-helix310-32112
α-helix3231
β-strand330-331251
α-helix339-34810
α-helix352-3543
β-strand358146
α-helix360-3656
α-helix368-3747
Chain b: 2 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand6-12737
α-helix15-3117
α-helix35-4915
β-strand54-681537
β-strand73-78637
β-strand81-87737
Chain B: 20 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix10-112
β-strand12-16556
β-strand20-25656
β-strand33-36456
β-strand39-42457
β-strand45-46258
β-strand57157
α-helix60-645
β-strand69-72457
β-strand75-76259
β-strand79-80259
α-helix83-9311
β-strand108-112556
α-helix118-1269
α-helix127-1315
β-strand136-141656
α-helix142-1509
β-strand155-160660
β-strand165-171760
β-strand174-175260
β-strand181-183360
α-helix187-19913
α-helix208-22013
β-strand223161
α-helix228-2336
α-helix235-2362
β-strand240-242362
β-strand248-250362
α-helix254-2574
α-helix258-2614
α-helix265-2684
α-helix275-28410
α-helix288-2958
β-strand298-301460
β-strand308161
α-helix310-32112
β-strand329-331360
α-helix339-34810
α-helix353-3553
β-strand358-359256
α-helix360-3656
α-helix368-3747

45 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Platelet-activating factor acetylhydrolase IB subunit beta1, 2, 3, 4protein410Homo sapiensP43034 (AlphaFold model)
ARP1 actin related protein 1 homolog AA, B, C, D, E, F, G, Iprotein376Sus scrofaF2Z5G5 (AlphaFold model)
Actin, cytoplasmic 1Hprotein375Sus scrofaQ6QAQ1 (AlphaFold model)
Arp11Jprotein417Sus scrofaI3LHK5 (AlphaFold model)
Capping protein (Actin filament) muscle Z-line, alpha 1Kprotein286Sus scrofaA0PFK5
F-actin-capping protein subunit betaLprotein272Sus scrofaA0PFK7
Dynactin subunit 2M, N, P, Qprotein405Sus scrofaA0A5G2QD80
Dynactin subunit 3O, Rprotein186Sus scrofaF1SEC0
Dynactin subunit 1S, Tprotein1281Sus scrofaA0A287B8J2
Dynactin 6Uprotein190Sus scrofaD0G6S1
Dynactin subunit 5Wprotein182Sus scrofaA0A286ZK88
C-Jun-amino-terminal kinase-interacting protein 3X, xprotein581Homo sapiensQ9UPT6

7 more molecules are not listed.

Sequence of entity 1 (1, 2, 3, 4), FASTA
>8PTK_1 Platelet-activating factor acetylhydrolase IB subunit beta (chains 1, 2, 3, 4)
MVLSQRQRDELNRAIADYLRSNGYEEAYSVFKKEAELDVNEELDKKYAGLLEKKWTSVIR
LQKKVMELESKLNEAKEEFTSGGPLGQKRDPKEWIPRPPEKYALSGHRSPVTRVIFHPVF
SVMVSASEDATIKVWDYETGDFERTLKGHTDSVQDISFDHSGKLLASCSADMTIKLWDFQ
GFECIRTMHGHDHNVSSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRMV
RPNQDGTLIASCSNDQTVRVWVVATKECKAELREHEHVVECISWAPESSYSSISEATGSE
TKKSGKPGPFLLSGSRDKTIKMWDVSTGMCLMTLVGHDNWVRGVLFHSGGKFILSCADDK
TLRVWDYKNKRCMKTLNAHEHFVTSLDFHKTAPYVVTGSVDQTVKVWECR
Sequence of entity 2 (A, B, C, D, E, F, G, I), FASTA
>8PTK_2 ARP1 actin related protein 1 homolog A (chains A, B, C, D, E, F, G, I)
MESYDVIANQPVVIDNGSGVIKAGFAGDQIPKYCFPNYVGRPKHVRVMAGALEGDIFIGP
KAEEHRGLLSIRYPMEHGIVKDWNDMERIWQYVYSKDQLQTFSEEHPVLLTEAPLNPRKN
RERAAEVFFETFNVPALFISMQAVLSLYATGRTTGVVLDSGDGVTHAVPIYEGFAMPHSI
MRIDIAGRDVSRFLRLYLRKEGYDFHSSSEFEIVKAIKERACYLSINPQKDETLETEKAQ
YYLPDGSTIEIGPSRFRAPELLFRPDLIGEESEGIHEVLVFAIQKSDMDLRRTLFSNIVL
SGGSTLFKGFGDRLLSEVKKLAPKDVKIRISAPQERLYSTWIGGSILASLDTFKKMWVSK
KEYEEDGARSIHRKTF
Sequence of entity 3 (H), FASTA
>8PTK_3 Actin, cytoplasmic 1 (chains H)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF
Sequence of entity 4 (J), FASTA
>8PTK_4 Arp11 (chains J)
MPLYEGLGSGGEKTAVVIDLGEAFTKCGFAGETGPRCIIPSVIKKAGMPKPIKVVQYNIN
TEELYSYLKEFIHILYFRHLLVNPRDRRVVVIESVLCPSHFRETLTRVLFKYFEVPSVLL
APSHLMALLTLGINSAMVLDCGYRESLVLPIYEGIPVLNCWGALPLGGKALHKELETQLL
EQCTVDTGAAKEQSLPSVMGSIPEGVLEDIKVRTCFVSDLTRGLKIQAAKFNIDGNTERP
SPPPNVDYPLDGEKILHVLGSIRDSVVEILFEQDNEEKSVATLILDSLMQCPIDTRKQLA
ENLVIIGGTSMLPGFLHRLLAEIRYLVEKPKYKKTLGTKTFRIHTPPAKANCVAWLGGAI
FGALQDILGSRSVSKEYYNQTGRIPDWCSLNNPPLEMVFDVGKSQPPLMKRAFSTEK
Sequence of entity 5 (K), FASTA
>8PTK_5 Capping protein (Actin filament) muscle Z-line, alpha 1 (chains K)
MADFEDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMD
QFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVDGSLKSW
RESCDSALRAYVKDHYSNGFCTVYAKNIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFT
ITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSVTVSNEAQTAKEFIKIIEHAENEYQ
TAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQNA
Sequence of entity 6 (L), FASTA
>8PTK_6 F-actin-capping protein subunit beta (chains L)
MSDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYL
LCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVY
LWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTN
KSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIV
NGLRSVQTFADKSKQEALKNDLVEALKRKQQC
Sequence of entity 7 (M, N, P, Q), FASTA
>8PTK_7 Dynactin subunit 2 (chains M, N, P, Q)
MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDAELEELTSTSVEHIIVNPNAAYDKFK
DKRVGTKGLDFSDRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQRLLHEVQELTTEVE
KIKMTVKESATEEKLTPVVLAKQLAALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLL
LQLEATKNTKGAGSGGKTTSGSPPDSSLVTYELHSRPEQDKFSQAAKVAELEKRLTELEA
TVRCDQDAQNPLSAGLQGACLMETVELLQAKVSALDLAVLDQVEARLQSVLGKVNEIAKH
KASVEDADTQSKVHQLYETIQRWSPIASTLPELVQRLVTIKQLHEQAMQFGQLLTHLDTT
QQMIACSLKDNATLLTQVQTTMRENLSTVEGNFANIDERMKKLGK
Sequence of entity 8 (O, R), FASTA
>8PTK_8 Dynactin subunit 3 (chains O, R)
MAGVTDVQRLQARLEELERWVYGPGGSRGSRKVADGLVKVQVALGNIASKRERVKILYKK
IEDLIKYLDPEYMDRIAIPDASKLQFILAEEQFILSQVALLEQVEALVPMLDSAHIKAVP
EHAARLQRLAQIHIQQQDQCVEITEESKALLEEYNKTTMLLSKQFVQWDELLCQLEAAKQ
VKPAEE
Sequence of entity 9 (S, T), FASTA
>8PTK_9 Dynactin subunit 1 (chains S, T)
MAQSKRHVYSRTPSGSRMSAEASARPLRVGSRVEVIGKGHRGTVAYVGATLFATGKWVGV
ILDEAKGKNDGTVQGRKYFTCDEGHGIFVRQSQIQVFEDGADTTSPETPDSSASKVLRRE
GTDSNAKTSKLRGPKPKKAPTARKTTTRRPKPTRPASTGVAGASSSLGPSGSASAGELSS
SEPSTPAQTPLAAPIIPTPALTSPGAAPPLPSPSKEEEGLRAQVRDLEEKLETLRLKRAE
DKAKLKELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADT
ADAIEMATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQL
KQLEEQNARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAE
STIDELKEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDELQENARE
TELELREQLDMAGARVREAQKRVEAAQETVADYQQTIKKYRQLTAHLQDVNRELTNQQEA
SVERQQQPPPETFDFKIKFAETKAHAKAIEMELRQMEVAQANRHMSLLTAFMPDSFLRPG
GDHDCVLVLLLMPRLICKAELIRKQAQEKFDLSENCSERPGLRGAAGEQLSFAAGLVYSL
SLLQATLHRYEHALSQCSVDVYKKVGSLYPEMSAHERSLDFLIELLHKDQLDETVNVEPL
TKAIKYYQHLYSIHLAEQPEDSTMQLADHIKFTQSALDCMSVEVGRLRAFLQGGQEASDI
ALLLRDLETSCSDIRQFCKKIRRRMPGTDAPGIPAALAFGAQVSDTLLDCRKHLTWVVAV
LQEVAAAAAQLIAPLAENEGLPVAALEELAFKASEQIYGTPSSSPYECLRQSCNILISTM
NKLATAMQEGEYDAERPPSKPPPVELRAAALRAEITDAEGLGLKLEDRETVIKELKKSLK
IKGEELSEANVRLSLLEKKLDSAAKDADERIEKVQTRLEETQALLRKKEKEFEETMDALQ
ADIDQLEAEKAELKQRLNSQSKRTIEGIRGPPPSGIATLVSGIAGEEQQRGGAPGQAPGI
VPGPGLVKDSPLLLQQISAMRLHISQLQHENSVLKGAQMKASLAALPPLHVAKLSLPPHE
GPGSELAAGALYRKTNQLLETLNQLSTHTHVVDITRSSPAAKSPSAQLLEQVTQLKSLSD
TIEKLKDEVLKETVSQRPGATVPTDFATFPSSAFLRAKEEQQDDTVYMGKVTFSCAAGLG
QRHRLVLTQEQLHQLHDRLIS
Sequence of entity 10 (U), FASTA
>8PTK_10 Dynactin 6 (chains U)
MAEKTQKSVKIAPGAVVCVESEIRGDVTIGPRTVIHPKARIIAEAGPIVIGEGNLIEEQA
LIINAHPDNITPDAEDSEPKPMIIGTNNVFEVGCYSQAMKMGDNNVIESKAYVGRNVILT
SGCIIGACCNLNTFEVIPENTVIYGADCLRRVQTERPQPQTLQLDFLMKILPNYHHLKKT
MKGSSTPVKN
Sequence of entity 11 (W), FASTA
>8PTK_11 Dynactin subunit 5 (chains W)
MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTIVMNDCIIRGDLANVRVGRH
CVVKSRSVIRPPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRC
VLKDCCKILDNTVLPPETVVPPFTVFSGCPGLFSGELPECTQELMIDVTKSYYQKFLPLT
QV
Sequence of entity 12 (X, x), FASTA
>8PTK_12 C-Jun-amino-terminal kinase-interacting protein 3 (chains X, x)
SNIEFLKMMEIQMDEGGGVVVYQDDYCSGSVMSERVSGLAGSIYREFERLIHCYDEEVVK
ELMPLVVNVLENLDSVLSENQEHEVELELLREDNEQLLTQYEREKALRRQAEEKFIEFED
ALEQEKKELQIQVEHYEFQTRQLELKAKNYADQISRLEERESEMKKEYNALHQRHTEMIQ
TYVEHIERSKMQQVGGNSQTESSLPGRRKERPTSLNVFPLADGTVRAQIGGKLVPAGDHW
HLSDLGQLQSSSSYQCPQDEMSESGQSSAAATPSTTGTKSNTPTSSVPSAAVTPLNESLQ
PLGDYGVGSKNSKRAREKRDSRNMEVQVTQEMRNVSIGMGSSDEWSDVQDIIDSTPELDM
CPETRLDRTGSSPTQGIVNKAFGINTDSLYHELSTAGSEVIGDVDEGADLLGEFSVRDDF
FGMGKEVGNLLLENSQLLETKNALNVVKNDLIAKVDQLSGEQEVLRGELEAAKQAKVKLE
NRIKELEEELKRVKSEAIIARREPKEEAEDVSSYLCTESDKIPMAQRRRFTRVEMARVLM
ERNQYKERLMELQEAVRWTEMIRASREGSGSGRWSHPQFEK

Ligands and cofactors

IDNameFormulaCopies
ANPPhosphoaminophosphonic acid-adenylate esterC10 H17 N6 O12 P34
MGMagnesium ionMg6
ZNZinc ionZn3
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P36
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P216

Primary citation

Molecular mechanism of dynein-dynactin complex assembly by LIS1. Singh, K., Lau, C.K., Manigrasso, G. et al. Science (2024) 383:eadk8544-eadk8544. DOI 10.1126/science.adk8544 · PubMed

Other PDB entries of the same protein (UniProt P43034 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

About this viewer

MolViewer shows 8PTK directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.