9DGV: Alpha-centractin

structure of dynactin, dynein tail with TRAK2 from dynein-dynactin-TRAK2 on microtubules. Determined by electron microscopy at 8.8 Å resolution. Released 10 Sept 2025.

Method
Electron microscopy
Resolution
8.8 Å
Organisms
Sus scrofa, Mus musculus
Chains
33
Atoms
86,528
Mol. weight
3704.75 kDa
Ligands
ADP, ATP, ZN
Released
10 Sept 2025

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

Secondary structure: helices and β-sheets

9DGV contains 524 α-helices and 496 β-strands across 33 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: 2 helices, 0 β-strands

ElementResiduesLengthSheet
α-helix115-15339
α-helix290-35162
Chain A: 24 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix10-112
β-strand12-1651
β-strand20-2561
β-strand33-3641
β-strand39-4242
β-strand45-4623
α-helix51-533
β-strand5712
α-helix60-645
β-strand69-7242
β-strand75-7624
β-strand79-8024
α-helix83-9412
β-strand108-11251
α-helix1131
α-helix118-13013
β-strand136-14161
α-helix142-1509
β-strand155-16065
β-strand165-17175
β-strand174-17525
α-helix177-1793
β-strand181-18335
α-helix187-20115
α-helix208-22013
β-strand22316
α-helix228-2336
α-helix235-2373
β-strand240-24237
β-strand248-25037
α-helix254-2574
α-helix258-2614
α-helix265-2673
α-helix275-28511
α-helix288-2969
β-strand298-30145
α-helix303-3064
β-strand30816
α-helix310-32112
α-helix3231
β-strand330-33125
α-helix339-34911
α-helix352-3565
β-strand358-35921
α-helix360-3667
α-helix368-3747
Chain b: 2 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix115-15440
α-helix290-35061
Chain B: 21 helices, 22 β-strands
ElementResiduesLengthSheet
β-strand12-15412
β-strand20-25612
β-strand33-36412
β-strand39-42413
β-strand45-46214
β-strand57113
α-helix60-645
β-strand69-72413
β-strand75-76215
β-strand79-80215
α-helix83-9311
α-helix103-1053
β-strand108-111412
α-helix118-13013
β-strand136-140512
α-helix143-1508
β-strand155-160616
β-strand165-171716
β-strand174-175216
β-strand181-183316
α-helix187-20115
α-helix208-22013
β-strand223117
α-helix228-2336
α-helix235-2362
β-strand240-242318
β-strand248-250318
α-helix254-2574
α-helix259-2624
α-helix265-2673
α-helix275-28511
α-helix288-2969
β-strand298-301416
α-helix303-3064
β-strand308117
α-helix310-32112
α-helix3231
β-strand328-331416
α-helix339-34911
α-helix353-3564
β-strand358-359212
α-helix360-3667
α-helix368-3736
Chain C: 22 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix10-112
β-strand12-15427
β-strand20-25627
β-strand33-36427
β-strand39-42428
β-strand45-46229
β-strand57128
α-helix60-645
β-strand69-72428
β-strand75-76230
β-strand79-80230
α-helix83-9311
α-helix103-1053
β-strand108-111427
α-helix118-1269
α-helix127-1315
β-strand136-140527
α-helix142-1509
β-strand155-16063
β-strand165-17173
β-strand174-17523
β-strand181-18333
α-helix187-20115
α-helix208-22013
β-strand223131
α-helix228-2336
β-strand240-242332
β-strand248-250332
α-helix254-2574
α-helix259-2624
α-helix265-2673
α-helix275-28511
α-helix291-2966
β-strand298-30143
α-helix303-3064
β-strand308131
α-helix310-32112
α-helix3231
β-strand330-33343
α-helix339-34911
α-helix352-3565
β-strand358-359227
α-helix360-3667
α-helix368-3725
Chain D: 21 helices, 22 β-strands
ElementResiduesLengthSheet
β-strand12-16542
β-strand20-25642
β-strand33-36442
β-strand39-42443
β-strand45-46244
β-strand57143
α-helix60-645
β-strand69-72443
β-strand75-76245
β-strand79-80245
α-helix83-9311
α-helix103-1053
β-strand108-112542
α-helix118-13013
β-strand136-141642
α-helix142-1509
β-strand155-160614
β-strand165-171714
β-strand174-175214
α-helix177-1793
β-strand181-183314
α-helix187-20115
α-helix208-22013
β-strand223146
α-helix228-2347
β-strand240-242347
β-strand248-250347
α-helix254-2574
α-helix259-2635
α-helix265-2673
α-helix275-28511
α-helix291-2966
β-strand298-301414
α-helix303-3064
β-strand308146
α-helix310-32112
α-helix3231
β-strand329-331314
α-helix339-34911
α-helix352-3565
β-strand358-359242
α-helix360-3667
α-helix368-3736
Chain e: 39 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix29-4214
α-helix50-567
α-helix59-7012
α-helix72-743
β-strand77-815139
β-strand83-864140
α-helix87-882
α-helix94-952
β-strand96-994140
β-strand102-1043139
β-strand114-1185139
α-helix131-1344
β-strand1381139
α-helix145-1517
α-helix152-1576
α-helix158-1669
α-helix178-19821
α-helix202-2054
α-helix213-22210
α-helix233-2353
α-helix239-26123
α-helix271-29323
α-helix295-30612
α-helix310-32011
α-helix322-33716
α-helix341-3466
α-helix350-36617
α-helix374-39926
α-helix401-4044
α-helix406-43530
α-helix455-48228
α-helix514-53017
α-helix540-57233
α-helix578-58710
α-helix595-62228
α-helix632-6387
α-helix643-66927
α-helix677-69317
α-helix696-70914
β-strand7191141
β-strand724-7252142
β-strand728-7314142
α-helix7351
β-strand7361141
α-helix741-75616
α-helix762-79736
α-helix799-8013
α-helix806-82015
α-helix829-84820
Chain E: 22 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix9-113
β-strand12-15451
β-strand20-25651
β-strand33-36451
β-strand39-42452
β-strand45-46253
β-strand57152
α-helix60-645
β-strand69-72452
β-strand75-76254
β-strand79-80254
α-helix83-9311
β-strand108-112551
α-helix1131
α-helix118-13013
β-strand136-141651
α-helix142-1509
β-strand155-160629
β-strand165-171729
β-strand174-175229
β-strand181-183329
α-helix187-20115
α-helix208-22013
β-strand223155
α-helix228-2336
α-helix235-2362
β-strand240-242356
β-strand248-250356
α-helix254-2574
α-helix259-2613
α-helix265-2684
α-helix275-28511
α-helix290-2967
β-strand298-301429
α-helix303-3064
β-strand308155
α-helix310-32112
α-helix3231
β-strand329-331329
α-helix339-34911
α-helix352-3565
β-strand358-359251
α-helix360-3667
α-helix368-3736

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Alpha-centractinA, B, C, D, E, F, G, Iprotein376Sus scrofaA0A8D1PMN0 (AlphaFold model)
Actin, cytoplasmic 1Hprotein375Sus scrofaQ6QAQ1 (AlphaFold model)
Actin-related protein 10Jprotein417Sus scrofaI3LHK5 (AlphaFold model)
F-actin-capping protein subunit alpha-1Kprotein286Sus scrofaA0PFK5 (AlphaFold model)
F-actin-capping protein subunit betaLprotein272Sus scrofaA0PFK7
Dynactin subunit 2M, N, P, Qprotein405Sus scrofaA0A5G2QD80
Dynactin subunit 3O, Rprotein186Sus scrofaF1SEC0
Dynactin subunit 6Uprotein190Sus scrofaD0G6S1
Dynactin subunit 5Vprotein182Sus scrofaA0A286ZK88
Dynactin subunit 1W, Zprotein1281Sus scrofaA0A287B8J2
Dynactin subunit 4Yprotein467Sus scrofaA0A4X1TB62
Trafficking protein, kinesin binding 2a, bprotein913Mus musculusQ6P9N8

2 more molecules are not listed.

Sequence of entity 1 (A, B, C, D, E, F, G, I), FASTA
>9DGV_1 Alpha-centractin (chains A, B, C, D, E, F, G, I)
MESYDVIANQPVVIDNGSGVIKAGFAGDQIPKYCFPNYVGRPKHVRVMAGALEGDIFIGP
KAEEHRGLLSIRYPMEHGIVKDWNDMERIWQYVYSKDQLQTFSEEHPVLLTEAPLNPRKN
RERAAEVFFETFNVPALFISMQAVLSLYATGRTTGVVLDSGDGVTHAVPIYEGFAMPHSI
MRIDIAGRDVSRFLRLYLRKEGYDFHSSSEFEIVKAIKERACYLSINPQKDETLETEKAQ
YYLPDGSTIEIGPSRFRAPELLFRPDLIGEESEGIHEVLVFAIQKSDMDLRRTLFSNIVL
SGGSTLFKGFGDRLLSEVKKLAPKDVKIRISAPQERLYSTWIGGSILASLDTFKKMWVSK
KEYEEDGARSIHRKTF
Sequence of entity 2 (H), FASTA
>9DGV_2 Actin, cytoplasmic 1 (chains H)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF
Sequence of entity 3 (J), FASTA
>9DGV_3 Actin-related protein 10 (chains J)
MPLYEGLGSGGEKTAVVIDLGEAFTKCGFAGETGPRCIIPSVIKKAGMPKPIKVVQYNIN
TEELYSYLKEFIHILYFRHLLVNPRDRRVVVIESVLCPSHFRETLTRVLFKYFEVPSVLL
APSHLMALLTLGINSAMVLDCGYRESLVLPIYEGIPVLNCWGALPLGGKALHKELETQLL
EQCTVDTGAAKEQSLPSVMGSIPEGVLEDIKVRTCFVSDLTRGLKIQAAKFNIDGNTERP
SPPPNVDYPLDGEKILHVLGSIRDSVVEILFEQDNEEKSVATLILDSLMQCPIDTRKQLA
ENLVIIGGTSMLPGFLHRLLAEIRYLVEKPKYKKTLGTKTFRIHTPPAKANCVAWLGGAI
FGALQDILGSRSVSKEYYNQTGRIPDWCSLNNPPLEMVFDVGKSQPPLMKRAFSTEK
Sequence of entity 4 (K), FASTA
>9DGV_4 F-actin-capping protein subunit alpha-1 (chains K)
MADFEDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMD
QFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVDGSLKSW
RESCDSALRAYVKDHYSNGFCTVYAKNIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFT
ITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSVTVSNEAQTAKEFIKIIEHAENEYQ
TAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQNA
Sequence of entity 5 (L), FASTA
>9DGV_5 F-actin-capping protein subunit beta (chains L)
MSDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYL
LCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVY
LWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTN
KSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIV
NGLRSVQTFADKSKQEALKNDLVEALKRKQQC
Sequence of entity 6 (M, N, P, Q), FASTA
>9DGV_6 Dynactin subunit 2 (chains M, N, P, Q)
MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDAELEELTSTSVEHIIVNPNAAYDKFK
DKRVGTKGLDFSDRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQRLLHEVQELTTEVE
KIKMTVKESATEEKLTPVVLAKQLAALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLL
LQLEATKNTKGAGSGGKTTSGSPPDSSLVTYELHSRPEQDKFSQAAKVAELEKRLTELEA
TVRCDQDAQNPLSAGLQGACLMETVELLQAKVSALDLAVLDQVEARLQSVLGKVNEIAKH
KASVEDADTQSKVHQLYETIQRWSPIASTLPELVQRLVTIKQLHEQAMQFGQLLTHLDTT
QQMIACSLKDNATLLTQVQTTMRENLSTVEGNFANIDERMKKLGK
Sequence of entity 7 (O, R), FASTA
>9DGV_7 Dynactin subunit 3 (chains O, R)
MAGVTDVQRLQARLEELERWVYGPGGSRGSRKVADGLVKVQVALGNIASKRERVKILYKK
IEDLIKYLDPEYMDRIAIPDASKLQFILAEEQFILSQVALLEQVEALVPMLDSAHIKAVP
EHAARLQRLAQIHIQQQDQCVEITEESKALLEEYNKTTMLLSKQFVQWDELLCQLEAAKQ
VKPAEE
Sequence of entity 8 (U), FASTA
>9DGV_8 Dynactin subunit 6 (chains U)
MAEKTQKSVKIAPGAVVCVESEIRGDVTIGPRTVIHPKARIIAEAGPIVIGEGNLIEEQA
LIINAHPDNITPDAEDSEPKPMIIGTNNVFEVGCYSQAMKMGDNNVIESKAYVGRNVILT
SGCIIGACCNLNTFEVIPENTVIYGADCLRRVQTERPQPQTLQLDFLMKILPNYHHLKKT
MKGSSTPVKN
Sequence of entity 9 (V), FASTA
>9DGV_9 Dynactin subunit 5 (chains V)
MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTIVMNDCIIRGDLANVRVGRH
CVVKSRSVIRPPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRC
VLKDCCKILDNTVLPPETVVPPFTVFSGCPGLFSGELPECTQELMIDVTKSYYQKFLPLT
QV
Sequence of entity 10 (W, Z), FASTA
>9DGV_10 Dynactin subunit 1 (chains W, Z)
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 11 (Y), FASTA
>9DGV_11 Dynactin subunit 4 (chains Y)
MASLLQSERVLYLVQGEKKVRAPLSQLYFCRYCSELRSLECVSHEVDSHYCPSCLENMPS
AEAKLKKNRCANCFDCPGCMHTLSTRATSISTQLPDDPAKTAVKKAYYLACGFCRWTSRD
VGMADKSVASGGWQEPDHPHTQRMNKLIEYYQQLAQKEKVERDRKKLARRRNYMPLAFSQ
HTIHVVDKYGLGTRLQRPRAGTTITALAGLSLKEGEDQKEIKIEPAQAVDEVEPLPEDYY
TRPVNLTEVTTLQQRLLQPDFQPICASQLYPRHKHLLIKRSLRCRQCEHNLSKPEFNPTS
IKFKIQLVAVNYIPEVRIMSIPNLRYMKESQVLLTLTNPVENLTHVTLLECEEGDPDDTN
STAKVSVPPTELVLAGKDAAAEYDELAEPQDFPDDPDVVAFRKANKVGVFIKVTPQREEG
DVTVCFKLKHDFKNLAAPIRPVEEADPGAEVSWLTQHVELSLGPLLP
Sequence of entity 12 (a, b), FASTA
>9DGV_12 Trafficking protein, kinesin binding 2 (chains a, b)
MSQSQNAIFKSRTGEANLMSSNHRDSESITDVCSNEDLPEVELVNLLEEQLPQYKLRVDS
LFLYENQDWAQSSHQQQDAPETLSPVLAEETFRYMILGTDRVEQMTKTYNDIDMVTHLLA
ERDRDLELAARIGQALLKRNHVLSEQNEALEEQLGQAFDQVNQLQHELSKKDELLRIVSI
ASEESETDSSCSTPLRFNESFSLSQGLLQLDMLHEKLRELEEENMALRSKACHIKTETFT
YEEKEQQLVNDCVKELRETNAQMSRMTEELSGKSDELLRYQEEISSLLSQIVDLQHKLKE
HVIEKEELRLHLQASKDAQRQLTMELHELQDRNMECLGMLHESQEEIKELRSKSGPSAHL
CFSQSYGVFTGESLAAEIEGTMRKKLSLDEESVSKQKAQQKRVFDTVKVANDTRGRSVTF
PVLLPIPGSNRSSVIMTAKPFESGVQPAEDKTLLSPGGSTEVPGNSQPTNPPGSPEDSDL
ATALHRLSLRRQNYLSEKQFFAEEWERKIQILAEQEEEVSSCDAPTENLASVCTDQSETT
DLGSASCLRGFMPEKLQIVKPLEGSQTLHHWQQLAQPNLGTILDPRPGVITKGFTQVPKD
VVYHISDLEEDEEEGITFQVQQPLQLEQKPALPTPVTGIFLPPMTSAGGPGTVATSNPGK
CLSFTNSTFTFTTCRILHPSDITQVTPSSGFPSLACGSSASSSSNTAVNSPAASYRLSIG
ESITNRRDSTITFSSTRSLAKLLQERGISAKVYHSPASENPLLQPCPKALATPSTPPNSP
AQSPCSSPLPFEPRVHVSENFLASRPAETFLQEMYGLRPSRAPPDVGQLKMNLVDRLKRL
GIARVVKTPDPQENGKSREAEMGLQKPDPAVYLNSGGSLLCGLRRNQSLPVMMGSFGAPV
CTTSPKMGILKED

Ligands and cofactors

IDNameFormulaCopies
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P29
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31
ZNZinc ionZn3

Primary citation

Roles of microtubules and LIS1 in dynein transport machinery assembly. Rao, Q., Yang, J., Chai, P. et al. Nature (2026) 652:1384-1392. DOI 10.1038/s41586-026-10153-y · PubMed

Other PDB entries of the same protein (UniProt A0A8D1PMN0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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