9HHL: Dynein-Dynactin-NuMA-LIS1

Structure of Dynein-Dynactin-NuMA-LIS1. Determined by electron microscopy at 6.53 Å resolution. Released 3 Dec 2025.

Method
Electron microscopy
Resolution
6.53 Å
Organisms
Homo sapiens, Sus scrofa
Chains
41
Atoms
64,583
Mol. weight
3953.07 kDa
Ligands
ZN, ATP, ADP
Released
3 Dec 2025

Explore 9HHL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HHL contains 568 α-helices and 530 β-strands across 41 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: 3 helices, 1 β-strand

ElementResiduesLengthSheet
α-helix212-26352
α-helix277-394118
β-strand407-408217
α-helix409-42416
Chain 2: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix212-26453
α-helix277-394118
α-helix409-42416
Chain A: 20 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix10-112
β-strand12-16528
β-strand20-25628
β-strand35-36228
β-strand39-42429
β-strand45-46230
β-strand57129
α-helix60-645
β-strand69-72429
β-strand75-76231
β-strand79-80231
α-helix83-9210
β-strand108-112528
α-helix118-1269
α-helix127-1315
β-strand136-141628
α-helix142-1498
β-strand155-160632
β-strand165-171732
β-strand174-175232
β-strand181-183332
α-helix187-20115
α-helix208-22013
β-strand223133
α-helix228-2336
β-strand240-242334
β-strand248-250334
α-helix254-2574
α-helix259-2613
α-helix265-2673
α-helix275-2839
α-helix288-2969
β-strand298-301432
α-helix304-3063
β-strand308133
α-helix310-31910
β-strand330-331232
α-helix339-34810
α-helix352-3543
β-strand358-359228
α-helix360-3656
α-helix368-3747
Chain B: 22 helices, 22 β-strands
ElementResiduesLengthSheet
β-strand12-16539
β-strand20-25639
β-strand33-36439
β-strand39-42440
β-strand45-46241
β-strand57140
α-helix60-645
α-helix66-683
β-strand69-72440
β-strand75-76242
β-strand79-80242
α-helix83-9311
α-helix103-1053
β-strand108-112539
α-helix118-1269
α-helix127-1315
β-strand136-141639
α-helix142-1509
β-strand155-160643
β-strand165-171743
β-strand174-175243
β-strand181-183343
α-helix187-20115
α-helix208-22013
β-strand223144
α-helix228-2336
α-helix235-2362
β-strand240-242345
β-strand248-250345
α-helix254-2574
α-helix258-2625
α-helix265-2684
α-helix275-28410
α-helix288-2958
β-strand298-301443
α-helix303-3064
β-strand308144
α-helix311-32111
β-strand328-331443
α-helix339-34911
α-helix353-3564
β-strand358-359239
α-helix360-3667
α-helix368-3747
Chain C: 22 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix10-112
β-strand12-165113
β-strand20-256113
β-strand33-364113
β-strand39-424114
β-strand45-46269
β-strand57-582114
α-helix60-645
β-strand69-724114
β-strand75-762115
β-strand79-802115
α-helix83-9311
β-strand108-1114113
α-helix112-1132
α-helix119-1268
α-helix127-1315
β-strand136-1405113
α-helix142-1509
β-strand155-160630
β-strand165-171730
β-strand174-175230
β-strand181-183330
α-helix187-20115
α-helix208-22013
β-strand2231116
α-helix228-2325
β-strand240-2423117
β-strand248-2503117
α-helix254-2574
α-helix258-2603
α-helix265-2673
α-helix275-28410
α-helix291-2966
β-strand298-301430
α-helix303-3053
β-strand3081116
α-helix310-32112
α-helix3231
β-strand330-333430
α-helix339-34810
α-helix353-3564
β-strand358-3592113
α-helix360-3667
α-helix369-3724
Chain D: 19 helices, 23 β-strands
ElementResiduesLengthSheet
β-strand12-15449
β-strand20-25649
β-strand33-36449
β-strand39-42450
β-strand45-46251
β-strand57150
α-helix60-645
β-strand69-72450
β-strand75-76252
β-strand79-80252
α-helix83-9311
β-strand108-111449
α-helix118-1269
α-helix127-1315
β-strand136-140549
α-helix142-1509
β-strand156-160553
β-strand165-168453
β-strand170-171241
β-strand174-175241
β-strand181-183353
α-helix187-20115
α-helix208-22114
β-strand223154
β-strand240-242355
β-strand248-250355
α-helix254-2574
α-helix259-2613
α-helix265-2673
α-helix275-28511
α-helix291-2966
β-strand297-301553
α-helix303-3064
β-strand308154
α-helix310-32112
α-helix3231
β-strand329-331353
α-helix339-34810
α-helix353-3564
β-strand358-359249
α-helix360-3667
α-helix368-3758
Chain e: 39 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix22-232
β-strand241135
α-helix25-262
α-helix27-3711
α-helix39-424
α-helix50-567
α-helix59-7012
β-strand76-8611136
α-helix93-953
β-strand96-1049136
β-strand113-1208136
β-strand1261135
β-strand135-1406136
α-helix145-1528
α-helix153-1575
α-helix158-16811
α-helix179-19820
α-helix201-2044
α-helix211-22212
α-helix229-2324
α-helix235-2373
α-helix239-26022
α-helix271-29222
α-helix295-30612
α-helix310-3145
α-helix315-3195
α-helix322-33615
α-helix341-3455
α-helix350-36415
α-helix374-39926
α-helix406-44035
α-helix457-48327
α-helix514-52916
α-helix540-57233
α-helix578-58710
α-helix597-62428
α-helix631-6388
α-helix643-66927
α-helix673-6753
α-helix677-69115
α-helix696-70914
β-strand7181137
β-strand721-7233138
β-strand732-7343138
β-strand7371137
α-helix741-75616
α-helix762-79736
α-helix806-82015
α-helix829-84820
Chain E: 23 helices, 23 β-strands
ElementResiduesLengthSheet
α-helix10-112
β-strand12-15464
β-strand20-25664
β-strand33-36464
β-strand39-42465
α-helix451
β-strand46166
β-strand57165
α-helix60-645
β-strand69-72465
β-strand75-76267
β-strand79-80267
α-helix83-9311
β-strand108-111464
α-helix118-1269
α-helix127-1315
β-strand136-140564
α-helix142-1509
β-strand155-160668
β-strand165-170668
β-strand171169
β-strand174-175269
β-strand181-183368
α-helix187-20115
α-helix208-22013
β-strand223170
α-helix228-2336
α-helix235-2373
β-strand240-242371
β-strand248-250371
α-helix254-2574
α-helix258-2614
α-helix265-2684
α-helix275-28511
α-helix291-2966
β-strand298-301468
α-helix303-3053
β-strand308170
α-helix310-32112
α-helix3231
β-strand329-331368
α-helix339-34911
α-helix353-3564
β-strand358-359264
α-helix360-3667
α-helix368-3747

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cytoplasmic dynein 1 intermediate chain 2g, h, o, pprotein612Homo sapiensQ13409 (AlphaFold model)
Nuclear mitotic apparatus protein 1,Methylated-DNA--protein-cysteine methyltransferase1, 2protein889Homo sapiensP16455 (AlphaFold model), Q14980 (AlphaFold model)
ARP1 actin related protein 1 homolog AA, B, C, D, E, F, G, Iprotein376Sus scrofaF2Z5G5 (AlphaFold model)
Actin, cytoplasmic 1Hprotein375Sus scrofaQ6QAQ1
Arp11Jprotein417Sus scrofaI3LHK5
Capping protein (Actin filament) muscle Z-line, alpha 1Kprotein286Sus scrofaA0PFK5
F-actin-capping protein subunit betaLprotein272Sus scrofaA0PFK7
Dynactin subunit 2M, N, P, Q, Vprotein405Sus scrofaA0A5G2QD80
Dynactin subunit 3O, Rprotein186Sus scrofaF1SEC0
Dynactin 6Uprotein190Sus scrofaD0G6S1
Dynactin subunit 5Wprotein182Sus scrofaA0A286ZK88
Dynactin subunit 4Yprotein467Sus scrofaA0A4X1TB62

4 more molecules are not listed.

Sequence of entity 1 (g, h, o, p), FASTA
>9HHL_1 Cytoplasmic dynein 1 intermediate chain 2 (chains g, h, o, p)
MSDKSELKAELERKKQRLAQIREEKKRKEEERKKKETDQKKEAVAPVQEESDLEKKRREA
EALLQSMGLTPESPIVPPPMSPSSKSVSTPSEAGSQDSGDGAVGSRRGPIKLGMAKITQV
DFPPREIVTYTKETQTPVMAQPKEDEEEDDDVVAPKPPIEPEEEKTLKKDEENDSKAPPH
ELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLS
LNRQFFDERWSKHRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPE
YVFHCQSAVMSATFAKFHPNLVVGGTYSGQIVLWDNRSNKRTPVQRTPLSAAAHTHPVYC
VNVVGTQNAHNLISISTDGKICSWSLDMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNN
FVVGSEEGSVYTACRHGSKAGISEMFEGHQGPITGIHCHAAVGAVDFSHLFVTSSFDWTV
KLWSTKNNKPLYSFEDNAGYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDTEVPTASIS
VEGNPALNRVRWTHSGREIAVGDSEGQIVIYDVGEQIAVPRNDEWARFGRTLAEINANRA
DAEEEAATRIPA
Sequence of entity 2 (1, 2), FASTA
>9HHL_2 Nuclear mitotic apparatus protein 1,Methylated-DNA--protein-cysteine methyltransferase (chains 1, 2)
MTLHATRGAALLSWVNSLHVADPVEAVLQLQDCSIFIKIIDRIHGTEEGQQILKQPVSER
LDFVCSFLQKNRKHPSSPECLVSAQKVLEGSELELAKMTMLLLYHSTMSSKSPRDWEQFE
YKIQAELAVILKFVLDHEDGLNLNEDLENFLQKAPVPSTCSSTFPEELSPPSHQAKREIR
FLELQKVASSSSGNNFLSGSPASPMGDILQTPQFQMRRLKKQLADERSNRDELELELAEN
RKLLTEKDAQIAMMQQRIDRLALLNEKQAASPLEPKELEELRDKNESLTMRLHETLKQCQ
DLKTEKSQMDRKINQLSEENGDLSFKLREFASHLQQLQDALNELTEEHSKATQEWLEKQA
QLEKELSAALQDKKCLEEKNEILQGKLSQLEEHLSQLQDNPPQEKGEVLGDVLQLETLKQ
EAATLAANNTQLQARVEMLETERGQQEAKLLAERGHFEEEKQQLSSLITDLQSSISNLSQ
AKEELEQASQAHGARLTAQVASLTSELTTLNATIQQQDQELAGLKQQAKEKQAQLAQTLQ
QQEQASQGLRHQVEQLSSSLKQKEQQLKEVAEKQEATRQDHAQQLATAAEEREASLRERD
AALKQLEALEKEKAAKLEILQQQLQVANEARDSAQTSVTQAQREKAELSRKVEELQACVE
TARQEQHEAQAQVAELELQLRSEQQKATEKERVAQEKDQLQEQLQGSMDKDCEMKRTTLD
SPLGKLELSGCEQGLHRIIFLGKGTSAADAVEVPAPAAVLGGPEPLMQATAWLNAYFHQP
EAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYSHLAALAGNPAATAAVKTA
LSGNPVPILIPCHRVVQGDLDVGGYEGGLAVKEWLLAHEGHRLGKPGLG
Sequence of entity 3 (A, B, C, D, E, F, G, I), FASTA
>9HHL_3 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 4 (H), FASTA
>9HHL_4 Actin, cytoplasmic 1 (chains H)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF
Sequence of entity 5 (J), FASTA
>9HHL_5 Arp11 (chains J)
MPLYEGLGSGGEKTAVVIDLGEAFTKCGFAGETGPRCIIPSVIKKAGMPKPIKVVQYNIN
TEELYSYLKEFIHILYFRHLLVNPRDRRVVVIESVLCPSHFRETLTRVLFKYFEVPSVLL
APSHLMALLTLGINSAMVLDCGYRESLVLPIYEGIPVLNCWGALPLGGKALHKELETQLL
EQCTVDTGAAKEQSLPSVMGSIPEGVLEDIKVRTCFVSDLTRGLKIQAAKFNIDGNTERP
SPPPNVDYPLDGEKILHVLGSIRDSVVEILFEQDNEEKSVATLILDSLMQCPIDTRKQLA
ENLVIIGGTSMLPGFLHRLLAEIRYLVEKPKYKKTLGTKTFRIHTPPAKANCVAWLGGAI
FGALQDILGSRSVSKEYYNQTGRIPDWCSLNNPPLEMVFDVGKSQPPLMKRAFSTEK
Sequence of entity 6 (K), FASTA
>9HHL_6 Capping protein (Actin filament) muscle Z-line, alpha 1 (chains K)
MADFEDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMD
QFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVDGSLKSW
RESCDSALRAYVKDHYSNGFCTVYAKNIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFT
ITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSVTVSNEAQTAKEFIKIIEHAENEYQ
TAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQNA
Sequence of entity 7 (L), FASTA
>9HHL_7 F-actin-capping protein subunit beta (chains L)
MSDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYL
LCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVY
LWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTN
KSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIV
NGLRSVQTFADKSKQEALKNDLVEALKRKQQC
Sequence of entity 8 (M, N, P, Q, V), FASTA
>9HHL_8 Dynactin subunit 2 (chains M, N, P, Q, V)
MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDAELEELTSTSVEHIIVNPNAAYDKFK
DKRVGTKGLDFSDRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQRLLHEVQELTTEVE
KIKMTVKESATEEKLTPVVLAKQLAALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLL
LQLEATKNTKGAGSGGKTTSGSPPDSSLVTYELHSRPEQDKFSQAAKVAELEKRLTELEA
TVRCDQDAQNPLSAGLQGACLMETVELLQAKVSALDLAVLDQVEARLQSVLGKVNEIAKH
KASVEDADTQSKVHQLYETIQRWSPIASTLPELVQRLVTIKQLHEQAMQFGQLLTHLDTT
QQMIACSLKDNATLLTQVQTTMRENLSTVEGNFANIDERMKKLGK
Sequence of entity 9 (O, R), FASTA
>9HHL_9 Dynactin subunit 3 (chains O, R)
MAGVTDVQRLQARLEELERWVYGPGGSRGSRKVADGLVKVQVALGNIASKRERVKILYKK
IEDLIKYLDPEYMDRIAIPDASKLQFILAEEQFILSQVALLEQVEALVPMLDSAHIKAVP
EHAARLQRLAQIHIQQQDQCVEITEESKALLEEYNKTTMLLSKQFVQWDELLCQLEAAKQ
VKPAEE
Sequence of entity 10 (U), FASTA
>9HHL_10 Dynactin 6 (chains U)
MAEKTQKSVKIAPGAVVCVESEIRGDVTIGPRTVIHPKARIIAEAGPIVIGEGNLIEEQA
LIINAHPDNITPDAEDSEPKPMIIGTNNVFEVGCYSQAMKMGDNNVIESKAYVGRNVILT
SGCIIGACCNLNTFEVIPENTVIYGADCLRRVQTERPQPQTLQLDFLMKILPNYHHLKKT
MKGSSTPVKN
Sequence of entity 11 (W), FASTA
>9HHL_11 Dynactin subunit 5 (chains W)
MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTIVMNDCIIRGDLANVRVGRH
CVVKSRSVIRPPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRC
VLKDCCKILDNTVLPPETVVPPFTVFSGCPGLFSGELPECTQELMIDVTKSYYQKFLPLT
QV
Sequence of entity 12 (Y), FASTA
>9HHL_12 Dynactin subunit 4 (chains Y)
MASLLQSERVLYLVQGEKKVRAPLSQLYFCRYCSELRSLECVSHEVDSHYCPSCLENMPS
AEAKLKKNRCANCFDCPGCMHTLSTRATSISTQLPDDPAKTAVKKAYYLACGFCRWTSRD
VGMADKSVASGGWQEPDHPHTQRMNKLIEYYQQLAQKEKVERDRKKLARRRNYMPLAFSQ
HTIHVVDKYGLGTRLQRPRAGTTITALAGLSLKEGEDQKEIKIEPAQAVDEVEPLPEDYY
TRPVNLTEVTTLQQRLLQPDFQPICASQLYPRHKHLLIKRSLRCRQCEHNLSKPEFNPTS
IKFKIQLVAVNYIPEVRIMSIPNLRYMKESQVLLTLTNPVENLTHVTLLECEEGDPDDTN
STAKVSVPPTELVLAGKDAAAEYDELAEPQDFPDDPDVVAFRKANKVGVFIKVTPQREEG
DVTVCFKLKHDFKNLAAPIRPVEEADPGAEVSWLTQHVELSLGPLLP

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn3
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P32
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P28

Primary citation

Activation and regulation of the dynein-dynactin-NuMA complex. Aslan, M., d'Amico, E.A., Cho, N.H. et al. Nat Chem Biol (2026) 22:1434-1445. DOI 10.1038/s41589-026-02156-7 · PubMed

Other PDB entries of the same protein (UniProt Q13409 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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