6ZNL: Dynactin complex

Cryo-EM structure of the dynactin complex. Determined by electron microscopy at 3.8 Å resolution. Released 29 Jul 2020.

Method
Electron microscopy
Resolution
3.8 Å
Organism
Sus scrofa
Chains
23
Atoms
52,864
Mol. weight
1097.75 kDa
Ligands
ADP, ATP, ZN
Released
29 Jul 2020

Explore 6ZNL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZNL contains 350 α-helices and 329 β-strands across 23 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: 23 helices, 22 β-strands

ElementResiduesLengthSheet
α-helix10-112
β-strand12-1541
β-strand20-2561
β-strand33-3641
β-strand39-4242
β-strand45-4623
α-helix51-533
β-strand57-5822
α-helix60-645
β-strand69-7242
β-strand75-7624
β-strand79-8024
α-helix83-9412
β-strand108-11141
α-helix112-1132
α-helix118-13013
β-strand136-14051
α-helix142-1509
β-strand155-16065
β-strand165-17175
β-strand174-17525
β-strand181-18335
α-helix187-20115
α-helix210-22011
β-strand22316
α-helix228-2336
α-helix235-2373
β-strand240-24237
β-strand248-25037
α-helix254-2574
α-helix259-2624
α-helix275-28511
α-helix288-2903
α-helix291-2966
β-strand298-30145
α-helix303-3053
β-strand30816
α-helix310-32112
α-helix3231
β-strand330-33125
α-helix339-34911
α-helix353-3564
β-strand358-35921
α-helix360-3667
α-helix368-3747
Chain B: 21 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix111
β-strand12-1548
β-strand20-2568
β-strand33-3648
β-strand39-4249
β-strand45-46210
β-strand57-5829
α-helix60-645
β-strand69-7249
β-strand75-76211
β-strand79-80211
α-helix83-9311
β-strand108-11258
α-helix1131
α-helix118-13013
β-strand136-14168
α-helix142-1509
β-strand155-160612
β-strand165-171712
β-strand174-175212
β-strand181-183312
α-helix187-20115
α-helix208-22013
β-strand223113
α-helix228-2336
β-strand240-242314
β-strand248-250314
α-helix254-2574
α-helix259-2624
α-helix265-2673
α-helix275-28511
α-helix291-2966
β-strand298-301412
α-helix303-3053
β-strand308113
α-helix310-32112
α-helix3231
β-strand328-331412
α-helix339-34911
α-helix353-3564
β-strand358-35928
α-helix360-3667
α-helix368-3736
Chain C: 21 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix10-112
β-strand12-15415
β-strand20-25615
β-strand33-36415
β-strand39-42416
β-strand45-46217
β-strand57-58216
α-helix60-645
β-strand69-72416
β-strand75-76218
β-strand79-80218
α-helix83-9311
β-strand108-111415
α-helix112-1132
α-helix118-13013
β-strand136-140515
α-helix142-1509
β-strand155-16063
β-strand165-17173
β-strand174-17523
β-strand181-18333
α-helix187-20115
α-helix208-22013
β-strand223119
α-helix228-2336
β-strand240-242320
β-strand248-250320
α-helix254-2574
α-helix259-2624
α-helix265-2673
α-helix275-28511
α-helix291-2966
β-strand298-30143
α-helix303-3053
β-strand308119
α-helix310-32112
α-helix3231
β-strand330-33233
α-helix339-34911
α-helix353-3564
β-strand358-359215
α-helix360-3667
α-helix368-3725
Chain D: 21 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix10-112
β-strand12-15421
β-strand20-25621
β-strand33-36421
β-strand39-42422
β-strand45-46223
β-strand57-58222
α-helix60-645
β-strand69-72422
β-strand75-76224
β-strand79-80224
α-helix83-9311
β-strand108-111421
α-helix112-1132
α-helix118-13013
β-strand136-140521
α-helix142-1509
β-strand155-160610
β-strand165-171710
β-strand174-175210
β-strand181-183310
α-helix187-20115
α-helix208-22013
β-strand223125
α-helix228-2347
β-strand240-242326
β-strand248-250326
α-helix254-2574
α-helix259-2624
α-helix265-2673
α-helix275-28511
α-helix291-2966
β-strand298-301410
α-helix303-3053
β-strand308125
α-helix310-32112
α-helix3231
β-strand329-331310
α-helix339-34911
α-helix353-3564
β-strand358-359221
α-helix360-3667
α-helix368-3736
Chain E: 21 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix9-113
β-strand12-15427
β-strand20-25627
β-strand33-36427
β-strand39-42428
β-strand45-46229
β-strand57-58228
α-helix60-645
β-strand69-72428
β-strand75-76230
β-strand79-80230
α-helix83-9311
β-strand108-111427
α-helix112-1132
α-helix118-13013
β-strand136-140527
α-helix142-1509
β-strand155-160617
β-strand165-171717
β-strand174-175217
β-strand181-183317
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-helix290-2967
β-strand298-301417
α-helix303-3053
β-strand308131
α-helix310-32112
α-helix3231
β-strand329-331317
α-helix339-34911
α-helix353-3564
β-strand358-359227
α-helix360-3667
α-helix368-3736
Chain F: 24 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix9-113
β-strand12-15433
β-strand20-25633
β-strand33-36433
β-strand39-42434
β-strand45135
α-helix461
α-helix52-532
β-strand57-58234
α-helix60-645
β-strand69-72434
β-strand75-76236
β-strand79-80236
α-helix83-9412
β-strand108-111433
α-helix112-1132
α-helix118-13013
β-strand136-140533
α-helix142-1509
β-strand155-160623
β-strand165-171723
β-strand174-175223
β-strand181-183323
α-helix187-20115
α-helix210-22011
β-strand223137
α-helix228-2336
α-helix235-2373
β-strand240-242338
β-strand248-250338
α-helix254-2574
α-helix259-2624
α-helix275-28511
α-helix288-2903
α-helix291-2966
β-strand298-301423
α-helix303-3053
β-strand308137
α-helix310-32112
α-helix3231
β-strand329-331323
α-helix339-34911
α-helix353-3564
β-strand358-359233
α-helix360-3667
α-helix368-3747
Chain G: 26 helices, 23 β-strands
ElementResiduesLengthSheet
α-helix10-112
β-strand12-15439
β-strand20-25639
β-strand33-36439
β-strand39-40240
β-strand41-42241
β-strand45142
α-helix461
α-helix52-532
β-strand57-58240
α-helix60-645
β-strand69-70241
α-helix711
β-strand75-76243
β-strand79-80243
α-helix83-9412
β-strand108-111439
α-helix112-1132
α-helix118-13013
β-strand136-140539
α-helix142-1509
β-strand155-160629
β-strand165-171729
β-strand174-175229
α-helix177-1793
β-strand181-183329
α-helix187-20115
α-helix210-22011
β-strand223144
α-helix228-2336
α-helix235-2373
β-strand240-242345
β-strand248-250345
α-helix254-2574
α-helix259-2624
α-helix275-28511
α-helix288-2903
α-helix291-2966
β-strand298-301429
α-helix303-3053
β-strand308144
α-helix310-32112
α-helix3231
β-strand330-333429
α-helix339-34911
α-helix353-3564
β-strand358-359239
α-helix360-3667
α-helix368-3747
Chain H: 22 helices, 19 β-strands
ElementResiduesLengthSheet
β-strand8-12546
β-strand16-21646
β-strand29-32446
β-strand35-38447
α-helix44-452
β-strand53-54247
α-helix56-605
β-strand65-68447
β-strand71-72248
β-strand75-76248
α-helix79-879
α-helix88-947
β-strand103-107546
α-helix113-12513
β-strand131-136646
α-helix137-1437
β-strand150-155635
β-strand160-166735
β-strand169-170235
α-helix172-1743
β-strand176-178335
α-helix182-19615
α-helix203-21614
α-helix223-23210
β-strand239-241349
β-strand247-249349
α-helix253-2564
α-helix259-2624
α-helix264-2663
α-helix274-28411
α-helix290-2956
β-strand297-298235
α-helix302-3043
α-helix309-32012
β-strand329-330235
α-helix338-34811
α-helix350-3545
α-helix3561
β-strand357-358246
α-helix359-3657
α-helix369-3724

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
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 (AlphaFold model)
F-actin capping protein beta subunitLprotein272Sus scrofaA0PFK7
Dynactin subunit 2M, N, m, nprotein405Sus scrofaA0A5G2QD80
Dynactin subunit 3O, oprotein186Sus scrofaF1SEC0
Dynactin 6Uprotein190Sus scrofaD0G6S1
Dynactin subunit 5Vprotein182Sus scrofaA0A286ZK88
Dynactin subunit 4Yprotein467Sus scrofaA0A4X1TB62
Dynactin subunit 1Z, zprotein1286Sus scrofaA0A287B8J2
Sequence of entity 1 (A, B, C, D, E, F, G, I), FASTA
>6ZNL_1 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 2 (H), FASTA
>6ZNL_2 Actin, cytoplasmic 1 (chains H)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF
Sequence of entity 3 (J), FASTA
>6ZNL_3 Arp11 (chains J)
MPLYEGLGSGGEKTAVVIDLGEAFTKCGFAGETGPRCIIPSVIKKAGMPKPIKVVQYNIN
TEELYSYLKEFIHILYFRHLLVNPRDRRVVVIESVLCPSHFRETLTRVLFKYFEVPSVLL
APSHLMALLTLGINSAMVLDCGYRESLVLPIYEGIPVLNCWGALPLGGKALHKELETQLL
EQCTVDTGAAKEQSLPSVMGSIPEGVLEDIKVRTCFVSDLTRGLKIQAAKFNIDGNTERP
SPPPNVDYPLDGEKILHVLGSIRDSVVEILFEQDNEEKSVATLILDSLMQCPIDTRKQLA
ENLVIIGGTSMLPGFLHRLLAEIRYLVEKPKYKKTLGTKTFRIHTPPAKANCVAWLGGAI
FGALQDILGSRSVSKEYYNQTGRIPDWCSLNNPPLEMVFDVGKSQPPLMKRAFSTEK
Sequence of entity 4 (K), FASTA
>6ZNL_4 Capping protein (Actin filament) muscle Z-line, alpha 1 (chains K)
MADFEDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMD
QFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVDGSLKSW
RESCDSALRAYVKDHYSNGFCTVYAKNIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFT
ITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSVTVSNEAQTAKEFIKIIEHAENEYQ
TAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQNA
Sequence of entity 5 (L), FASTA
>6ZNL_5 F-actin capping protein beta subunit (chains L)
MSDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYL
LCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVY
LWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTN
KSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIV
NGLRSVQTFADKSKQEALKNDLVEALKRKQQC
Sequence of entity 6 (M, N, m, n), FASTA
>6ZNL_6 Dynactin subunit 2 (chains M, N, m, n)
MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDAELEELTSTSVEHIIVNPNAAYDKFK
DKRVGTKGLDFSDRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQRLLHEVQELTTEVE
KIKMTVKESATEEKLTPVVLAKQLAALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLL
LQLEATKNTKGAGSGGKTTSGSPPDSSLVTYELHSRPEQDKFSQAAKVAELEKRLTELEA
TVRCDQDAQNPLSAGLQGACLMETVELLQAKVSALDLAVLDQVEARLQSVLGKVNEIAKH
KASVEDADTQSKVHQLYETIQRWSPIASTLPELVQRLVTIKQLHEQAMQFGQLLTHLDTT
QQMIACSLKDNATLLTQVQTTMRENLSTVEGNFANIDERMKKLGK
Sequence of entity 7 (O, o), FASTA
>6ZNL_7 Dynactin subunit 3 (chains O, o)
MAGVTDVQRLQARLEELERWVYGPGGSRGSRKVADGLVKVQVALGNIASKRERVKILYKK
IEDLIKYLDPEYMDRIAIPDASKLQFILAEEQFILSQVALLEQVEALVPMLDSAHIKAVP
EHAARLQRLAQIHIQQQDQCVEITEESKALLEEYNKTTMLLSKQFVQWDELLCQLEAAKQ
VKPAEE
Sequence of entity 8 (U), FASTA
>6ZNL_8 Dynactin 6 (chains U)
MAEKTQKSVKIAPGAVVCVESEIRGDVTIGPRTVIHPKARIIAEAGPIVIGEGNLIEEQA
LIINAHPDNITPDAEDSEPKPMIIGTNNVFEVGCYSQAMKMGDNNVIESKAYVGRNVILT
SGCIIGACCNLNTFEVIPENTVIYGADCLRRVQTERPQPQTLQLDFLMKILPNYHHLKKT
MKGSSTPVKN
Sequence of entity 9 (V), FASTA
>6ZNL_9 Dynactin subunit 5 (chains V)
MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTIVMNDCIIRGDLANVRVGRH
CVVKSRSVIRPPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRC
VLKDCCKILDNTVLPPETVVPPFTVFSGCPGLFSGELPECTQELMIDVTKSYYQKFLPLT
QV
Sequence of entity 10 (Y), FASTA
>6ZNL_10 Dynactin subunit 4 (chains Y)
MASLLQSERVLYLVQGEKKVRAPLSQLYFCRYCSELRSLECVSHEVDSHYCPSCLENMPS
AEAKLKKNRCANCFDCPGCMHTLSTRATSISTQLPDDPAKTAVKKAYYLACGFCRWTSRD
VGMADKSVASGGWQEPDHPHTQRMNKLIEYYQQLAQKEKVERDRKKLARRRNYMPLAFSQ
HTIHVVDKYGLGTRLQRPRAGTTITALAGLSLKEGEDQKEIKIEPAQAVDEVEPLPEDYY
TRPVNLTEVTTLQQRLLQPDFQPICASQLYPRHKHLLIKRSLRCRQCEHNLSKPEFNPTS
IKFKIQLVAVNYIPEVRIMSIPNLRYMKESQVLLTLTNPVENLTHVTLLECEEGDPDDTN
STAKVSVPPTELVLAGKDAAAEYDELAEPQDFPDDPDVVAFRKANKVGVFIKVTPQREEG
DVTVCFKLKHDFKNLAAPIRPVEEADPGAEVSWLTQHVELSLGPLLP
Sequence of entity 11 (Z, z), FASTA
>6ZNL_11 Dynactin subunit 1 (chains Z, z)
MAQSKRHVYSRTPSGSRMSAEASARPLRVGSRVEVIGKGHRGTVAYVGATLFATGKWVGV
ILDEAKGKNDGTVQGRKYFTCDEGHGIFVRQSQIQVFEDGADTTSPETPDSSASKVLRRE
GTDSNAKTSKLRGPKPKKAPTARKTTTRRPKPTRPASTGVAGASSSLGPSGSASAGELSS
SEPSTPAQTPLAAPIIPTPALTSPGAAPPLPSPSKEEEGLRAQVRDLEEKLETLRLKRAE
DKAKLKELEKHKIQLEQVQEWKSKMQEQQADLQRRLKEARKEAKEALEAKERYMEEMADT
ADAIEMATLDKEMAEERAESLQQEVEALKERVDELTTDLEILKAEIEEKGSDGAASSYQL
KQLEEQNARLKDALVRMRDLSSSEKQEHVKLQKLMEKKNQELEVVRQQRERLQEELSQAE
STIDELKEQVDAALGAEEMVEMLTDRNLNLEEKVRELRETVGDLEAMNEMNDELQENARE
TELELREQLDMAGARVREAQKRVEAAQETVADYQQTIKKYRQLTAHLQDVNRELTNQQEA
SVERQQQPPPETFDFKIKFAETKAHAKAIEMELRQMEVAQANRHMSLLTAFMPDSFLRPG
GDHDCVLVLLLMPRLICKAELIRKQAQEKFDLSENCSERPGLRGAAGEQLSFAAGLVYSL
SLLQATLHRYEHALSQCSVDVYKKVGSLYPEMSAHERSLDFLIELLHKDQLDETVNVEPL
TKAIKYYQHLYSIHLAEQPEDSTMQLADHIKFTQSALDCMSVEVGRLRAFLQGGQEASDI
ALLLRDLETSCSDIRQFCKKIRRRMPGTDAPGIPAALAFGAQVSDTLLDCRKHLTWVVAV
LQEVAAAAAQLIAPLAENEGLPVAALEELAFKASEQVGWDGWAEGSAGGVRWPVWDFHHC
XKLLLVVGGLGGKRREFGEHHPAEKPPPVELRAAALRAEITDAEGLGLKLEDRETVIKEL
KKSLKIKGEELSEANVRLSLLEKKLDSAAKDADERIEKVQTRLEETQALLRKKEKEFEET
MDALQADIDQLEAEKAELKQRLNSQSKRTIEGIRGPPPSGIATLVSGIAGEEQQRGGAPG
QAPGIVPGPGLVKDSPLLLQQISAMRLHISQLQHENSVLKGAQMKASLAALPPLHVAKLS
LPPHEGPGSELAAGALYRKTNQLLETLNQLSTHTHVVDITRSSPAAKSPSAQLLEQVTQL
KSLSDTIEKLKDEVLKETVSQRPGATVPTDFATFPSSAFLRAKEEQQDDTVYMGKVTFSC
AAGLGQRHRLVLTQEQLHQLHDRLIS

Ligands and cofactors

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

Primary citation

Cryo-EM reveals the complex architecture of dynactin's shoulder region and pointed end. Lau, C.K., O'Reilly, F.J., Santhanam, B. et al. EMBO J (2021) 40:e106164-e106164. DOI 10.15252/embj.2020106164 · PubMed

Other PDB entries of the same protein (UniProt F2Z5G5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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