7Z8J: Cytoplasmic dynein

Cytoplasmic dynein (A2) bound to BICDR1. Determined by electron microscopy at 3.93 Å resolution. Released 27 Jul 2022.

Method
Electron microscopy
Resolution
3.93 Å
Organisms
Mus musculus, Homo sapiens
Chains
9
Atoms
20,189
Mol. weight
1981.44 kDa
Released
27 Jul 2022

Explore 7Z8J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z8J contains 93 α-helices and 79 β-strands across 9 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 f: 32 helices, 6 β-strands

ElementResiduesLengthSheet
α-helix271-28212
α-helix333-3364
α-helix341-3466
α-helix350-36415
α-helix365-3695
α-helix374-39926
α-helix406-44035
α-helix455-48329
α-helix514-53118
α-helix540-57435
α-helix578-58710
α-helix590-5923
α-helix598-62427
α-helix631-6388
α-helix643-66927
α-helix673-6753
α-helix677-69216
α-helix696-70914
β-strand71611
β-strand718-72472
β-strand731-73772
α-helix741-75616
α-helix762-77312
α-helix775-79723
α-helix799-8024
α-helix806-81914
β-strand82311
α-helix829-86335
α-helix864-8663
α-helix871-89121
α-helix896-92631
α-helix975-99420
β-strand99713
α-helix998-9992
α-helix1014-10174
β-strand101813
α-helix1020-10256
α-helix1031-104717
Chain h: 7 helices, 32 β-strands
ElementResiduesLengthSheet
β-strand265-27174
β-strand282-28765
β-strand294-29965
β-strand311-31775
β-strand327-33155
α-helix3341
β-strand335-34066
β-strand347-35266
β-strand357-36156
β-strand371-37226
β-strand386-39277
β-strand395-40177
β-strand406-41057
β-strand41118
β-strand41418
β-strand420-42347
β-strand42519
β-strand43119
β-strand434-438510
β-strand446-451610
β-strand456-460510
β-strand467-472610
β-strand479-484611
β-strand496-501611
β-strand506-510511
β-strand519-520211
β-strand527-532612
β-strand539-544612
β-strand548-553612
β-strand563-566412
α-helix5671
α-helix571-5722
β-strand573-57864
β-strand584-58964
β-strand594-59964
α-helix6001
α-helix601-6044
α-helix606-6072
α-helix610-62011
Chain j: 14 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix113-1219
β-strand133-138613
α-helix142-1443
α-helix145-16319
α-helix167-18216
β-strand227-232613
α-helix234-2363
α-helix237-2437
α-helix248-26518
β-strand268-271413
β-strand273114
β-strand278114
α-helix280-29213
β-strand301113
β-strand309-310213
α-helix317-32610
α-helix336-3394
α-helix350-3523
α-helix356-3583
α-helix359-37214
α-helix427-43812
Chain m: 25 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix271-29121
α-helix323-33715
α-helix342-3454
α-helix350-36415
α-helix365-3695
α-helix374-39825
α-helix406-44035
α-helix442-4443
α-helix457-48226
α-helix514-53219
α-helix540-57435
α-helix578-58710
α-helix590-5934
α-helix595-6006
α-helix603-62422
α-helix631-6388
α-helix643-66927
α-helix673-6753
α-helix679-69214
α-helix696-70914
β-strand716115
β-strand718-719216
β-strand736-737216
α-helix742-75615
α-helix762-79736
α-helix799-8024
α-helix806-82015
β-strand823115
α-helix829-85022
Chain n: 8 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix466-48015
α-helix518-53013
α-helix547-57428
α-helix578-58710
α-helix597-61519
α-helix662-6665
α-helix673-6753
α-helix677-6804
Chain o: 4 helices, 30 β-strands
ElementResiduesLengthSheet
β-strand265-271717
β-strand282-287618
β-strand294-299618
β-strand311-317718
β-strand327-331518
β-strand338-340319
β-strand347-350419
β-strand358-361419
β-strand371-372219
β-strand384-392920
β-strand395-402820
β-strand406-410520
β-strand420-423420
β-strand425121
β-strand431121
β-strand434-438522
β-strand446-451622
β-strand456-460522
β-strand467-472622
β-strand479-484623
β-strand496-501623
β-strand505-510623
β-strand518-520323
β-strand527-532624
β-strand539-544624
β-strand548-553624
β-strand563-566424
β-strand573-578617
β-strand584-589617
β-strand594-599617
α-helix6001
α-helix601-6044
α-helix606-6072
α-helix610-62011
Chain r: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix427-43812
Chains x and X: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix101-19191

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
BICD family-like cargo adapter 1X, xprotein577Mus musculusA0JNT9 (AlphaFold model)
Cytoplasmic dynein 1 heavy chain 1f, m, nprotein4646Homo sapiensQ14204
Cytoplasmic dynein 1 intermediate chain 2h, oprotein638Homo sapiensQ13409 (AlphaFold model)
Cytoplasmic dynein 1 light intermediate chain 2j, rprotein492Homo sapiensO43237 (AlphaFold model)
Sequence of entity 1 (X, x), FASTA
>7Z8J_1 BICD family-like cargo adapter 1 (chains X, x)
MSAFCLGLAGRASAPAEPDSACCMELPAGAGDAVRSPATAAALVSFPGGPGELELALEEE
LALLAAGERSSEPGEHPQAEPESPVEGHGPPLPPPPTQDPELLSVIRQKEKDLVLAARLG
KALLERNQDMSRQYEQMHKELTDKLEHLEQEKHELRRRFENREGEWEGRVSELETDVKQL
QDELERQQLHLREADREKTRAVQELSEQNQRLLDQLSRASEVERQLSMQVHALKEDFREK
NSSTNQHIIRLESLQAEIKMLSDRKRELEHRLSATLEENDLLQGTVEELQDRVLILERQG
HDKDLQLHQSQLELQEVRLSYRQLQGKVEELTEERSLQSSAATSTSLLSEIEQSMEAEEL
EQEREQLRLQLWEAYCQVRYLCSHLRGNDSADSAVSTDSSMDESSETSSAKDVPAGSLRT
ALNDLKRLIQSIVDGVEPTVTLLSVEMTALKEERDRLRVTSEDKEPKEQLQKAIRDRDEA
IAKKNAVELELAKCKMDMMSLNSQLLDAIQQKLNLSQQLEAWQDDMHRVIDRQLMDTHLK
EQSRPAAAAFPRGHGVGRGQEPSTADGKRLFSFFRKI
Sequence of entity 2 (f, m, n), FASTA
>7Z8J_2 Cytoplasmic dynein 1 heavy chain 1 (chains f, m, n)
MSEPGGGGGEDGSAGLEVSAVQNVADVSVLQKHLRKLVPLLLEDGGEAPAALEAALEEKS
ALEQMRKFLSDPQVHTVLVERSTLKEDVGDEGEEEKEFISYNINIDIHYGVKSNSLAFIK
RTPVIDADKPVSSQLRVLTLSEDSPYETLHSFISNAVAPFFKSYIRESGKADRDGDKMAP
SVEKKIAELEMGLLHLQQNIEIPEISLPIHPMITNVAKQCYERGEKPKVTDFGDKVEDPT
FLNQLQSGVNRWIREIQKVTKLDRDPASGTALQEISFWLNLERALYRIQEKRESPEVLLT
LDILKHGKRFHATVSFDTDTGLKQALETVNDYNPLMKDFPLNDLLSATELDKIRQALVAI
FTHLRKIRNTKYPIQRALRLVEAISRDLSSQLLKVLGTRKLMHVAYEEFEKVMVACFEVF
QTWDDEYEKLQVLLRDIVKRKREENLKMVWRINPAHRKLQARLDQMRKFRRQHEQLRAVI
VRVLRPQVTAVAQQNQGEVPEPQDMKVAEVLFDAADANAIEEVNLAYENVKEVDGLDVSK
EGTEAWEAAMKRYDERIDRVETRITARLRDQLGTAKNANEMFRIFSRFNALFVRPHIRGA
IREYQTQLIQRVKDDIESLHDKFKVQYPQSQACKMSHVRDLPPVSGSIIWAKQIDRQLTA
YMKRVEDVLGKGWENHVEGQKLKQDGDSFRMKLNTQEIFDDWARKVQQRNLGVSGRIFTI
ESTRVRGRTGNVLKLKVNFLPEIITLSKEVRNLKWLGFRVPLAIVNKAHQANQLYPFAIS
LIESVRTYERTCEKVEERNTISLLVAGLKKEVQALIAEGIALVWESYKLDPYVQRLAETV
FNFQEKVDDLLIIEEKIDLEVRSLETCMYDHKTFSEILNRVQKAVDDLNLHSYSNLPIWV
NKLDMEIERILGVRLQAGLRAWTQVLLGQAEDKAEVDMDTDAPQVSHKPGGEPKIKNVVH
ELRITNQVIYLNPPIEECRYKLYQEMFAWKMVVLSLPRIQSQRYQVGVHYELTEEEKFYR
NALTRMPDGPVALEESYSAVMGIVSEVEQYVKVWLQYQCLWDMQAENIYNRLGEDLNKWQ
ALLVQIRKARGTFDNAETKKEFGPVVIDYGKVQSKVNLKYDSWHKEVLSKFGQMLGSNMT
EFHSQISKSRQELEQHSVDTASTSDAVTFITYVQSLKRKIKQFEKQVELYRNGQRLLEKQ
RFQFPPSWLYIDNIEGEWGAFNDIMRRKDSAIQQQVANLQMKIVQEDRAVESRTTDLLTD
WEKTKPVTGNLRPEEALQALTIYEGKFGRLKDDREKCAKAKEALELTDTGLLSGSEERVQ
VALEELQDLKGVWSELSKVWEQIDQMKEQPWVSVQPRKLRQNLDALLNQLKSFPARLRQY
ASYEFVQRLLKGYMKINMLVIELKSEALKDRHWKQLMKRLHVNWVVSELTLGQIWDVDLQ
KNEAIVKDVLLVAQGEMALEEFLKQIREVWNTYELDLVNYQNKCRLIRGWDDLFNKVKEH
INSVSAMKLSPYYKVFEEDALSWEDKLNRIMALFDVWIDVQRRWVYLEGIFTGSADIKHL
LPVETQRFQSISTEFLALMKKVSKSPLVMDVLNIQGVQRSLERLADLLGKIQKALGEYLE
RERSSFPRFYFVGDEDLLEIIGNSKNVAKLQKHFKKMFAGVSSIILNEDNSVVLGISSRE
GEEVMFKTPVSITEHPKINEWLTLVEKEMRVTLAKLLAESVTEVEIFGKATSIDPNTYIT
WIDKYQAQLVVLSAQIAWSENVETALSSMGGGGDAAPLHSVLSNVEVTLNVLADSVLMEQ
PPLRRRKLEHLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPKQTDVLQQLSIQ
MANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEARLGGSPFGPAGTGKTESVKALG
HQLGRFVLVFNCDETFDFQAMGRIFVGLCQVGAWGCFDEFNRLEERMLSAVSQQVQCIQE
ALREHSNPNYDKTSAPITCELLNKQVKVSPDMAIFITMNPGYAGRSNLPDNLKKLFRSLA
MTKPDRQLIAQVMLYSQGFRTAEVLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLVSA
GNVKRERIQKIKREKEERGEAVDEGEIAENLPEQEILIQSVCETMVPKLVAEDIPLLFSL
LSDVFPGVQYHRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINHGL
MMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAISKDHLYGTLDPNTREWTDGLF
THVLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSVLDDNKLLTLPNGERLSLPPNVR
IMFEVQDLKYATLATVSRCGMVWFSEDVLSTDMIFNNFLARLRSIPLDEGEDEAQRRRKG
KEDEGEEAASPMLQIQRDAATIMQPYFTSNGLVTKALEHAFQLEHIMDLTRLRCLGSLFS
MLHQACRNVAQYNANHPDFPMQIEQLERYIQRYLVYAILWSLSGDSRLKMRAELGEYIRR
ITTVPLPTAPNIPIIDYEVSISGEWSPWQAKVPQIEVETHKVAAPDVVVPTLDTVRHEAL
LYTWLAEHKPLVLCGPPGSGKTMTLFSALRALPDMEVVGLNFSSATTPELLLKTFDHYCE
YRRTPNGVVLAPVQLGKWLVLFCDEINLPDMDKYGTQRVISFIRQMVEHGGFYRTSDQTW
VKLERIQFVGACNPPTDPGRKPLSHRFLRHVPVVYVDYPGPASLTQIYGTFNRAMLRLIP
SLRTYAEPLTAAMVEFYTMSQERFTQDTQPHYIYSPREMTRWVRGIFEALRPLETLPVEG
LIRIWAHEALRLFQDRLVEDEERRWTDENIDTVALKHFPNIDREKAMSRPILYSNWLSKD
YIPVDQEELRDYVKARLKVFYEEELDVPLVLFNEVLDHVLRIDRIFRQPQGHLLLIGVSG
AGKTTLSRFVAWMNGLSVYQIKVHRKYTGEDFDEDLRTVLRRSGCKNEKIAFIMDESNVL
DSGFLERMNTLLANGEVPGLFEGDEYATLMTQCKEGAQKEGLMLDSHEELYKWFTSQVIR
NLHVVFTMNPSSEGLKDRAATSPALFNRCVLNWFGDWSTEALYQVGKEFTSKMDLEKPNY
IVPDYMPVVYDKLPQPPSHREAIVNSCVFVHQTLHQANARLAKRGGRTMAITPRHYLDFI
NHYANLFHEKRSELEEQQMHLNVGLRKIKETVDQVEELRRDLRIKSQELEVKNAAANDKL
KKMVKDQQEAEKKKVMSQEIQEQLHKQQEVIADKQMSVKEDLDKVEPAVIEAQNAVKSIK
KQHLVEVRSMANPPAAVKLALESICLLLGESTTDWKQIRSIIMRENFIPTIVNFSAEEIS
DAIREKMKKNYMSNPSYNYEIVNRASLACGPMVKWAIAQLNYADMLKRVEPLRNELQKLE
DDAKDNQQKANEVEQMIRDLEASIARYKEEYAVLISEAQAIKADLAAVEAKVNRSTALLK
SLSAERERWEKTSETFKNQMSTIAGDCLLSAAFIAYAGYFDQQMRQNLFTTWSHHLQQAN
IQFRTDIARTEYLSNADERLRWQASSLPADDLCTENAIMLKRFNRYPLIIDPSGQATEFI
MNEYKDRKITRTSFLDDAFRKNLESALRFGNPLLVQDVESYDPVLNPVLNREVRRTGGRV
LITLGDQDIDLSPSFVIFLSTRDPTVEFPPDLCSRVTFVNFTVTRSSLQSQCLNEVLKAE
RPDVDEKRSDLLKLQGEFQLRLRQLEKSLLQALNEVKGRILDDDTIITTLENLKREAAEV
TRKVEETDIVMQEVETVSQQYLPLSTACSSIYFTMESLKQIHFLYQYSLQFFLDIYHNVL
YENPNLKGVTDHTQRLSIITKDLFQVAFNRVARGMLHQDHITFAMLLARIKLKGTVGEPT
YDAEFQHFLRGNEIVLSAGSTPRIQGLTVEQAEAVVRLSCLPAFKDLIAKVQADEQFGIW
LDSSSPEQTVPYLWSEETPATPIGQAIHRLLLIQAFRPDRLLAMAHMFVSTNLGESFMSI
MEQPLDLTHIVGTEVKPNTPVLMCSVPGYDASGHVEDLAAEQNTQITSIAIGSAEGFNQA
DKAINTAVKSGRWVMLKNVHLAPGWLMQLEKKLHSLQPHACFRLFLTMEINPKVPVNLLR
AGRIFVFEPPPGVKANMLRTFSSIPVSRICKSPNERARLYFLLAWFHAIIQERLRYAPLG
WSKKYEFGESDLRSACDTVDTWLDDTAKGRQNISPDKIPWSALKTLMAQSIYGGRVDNEF
DQRLLNTFLERLFTTRSFDSEFKLACKVDGHKDIQMPDGIRREEFVQWVELLPDTQTPSW
LGLPNNAERVLLTTQGVDMISKMLKMQMLEDEDDLAYAETEKKTRTDSTSDGRPAWMRTL
HTTASNWLHLIPQTLSHLKRTVENIKDPLFRFFEREVKMGAKLLQDVRQDLADVVQVCEG
KKKQTNYLRTLINELVKGILPRSWSHYTVPAGMTVIQWVSDFSERIKQLQNISLAAASGG
AKELKNIHVCLGGLFVPEAYITATRQYVAQANSWSLEELCLEVNVTTSQGATLDACSFGV
TGLKLQGATCNNNKLSLSNAISTALPLTQLRWVKQTNTEKKASVVTLPVYLNFTRADLIF
TVDFEIATKEDPRSFYERGVAVLCTE
Sequence of entity 3 (h, o), FASTA
>7Z8J_3 Cytoplasmic dynein 1 intermediate chain 2 (chains h, o)
MSDKSELKAELERKKQRLAQIREEKKRKEEERKKKETDQKKEAVAPVQEESDLEKKRREA
EALLQSMGLTPESPIVFSEYWVPPPMSPSSKSVSTPSEAGSQDSGDGAVGSRTLHWDTDP
SVLQLHSDSDLGRGPIKLGMAKITQVDFPPREIVTYTKETQTPVMAQPKEDEEEDDDVVA
PKPPIEPEEEKTLKKDEENDSKAPPHELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQ
INIFFDYSGRDLEDKEGEIQAGAKLSLNRQFFDERWSKHRVVSCLDWSSQYPELLVASYN
NNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLVVGGTYSGQIVLW
DNRSNKRTPVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSLDMLSHPQD
SMELVHKQSKAVAVTSMSFPVGDVNNFVVGSEEGSVYTACRHGSKAGISEMFEGHQGPIT
GIHCHAAVGAVDFSHLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALF
ACVDGMGRLDLWNLNNDTEVPTASISVEGNPALNRVRWTHSGREIAVGDSEGQIVIYDVG
EQIAVPRNDEWARFGRTLAEINANRADAEEEAATRIPA
Sequence of entity 4 (j, r), FASTA
>7Z8J_4 Cytoplasmic dynein 1 light intermediate chain 2 (chains j, r)
MAPVGVEKKLLLGPNGPAVAAAGDLTSEEEEGQSLWSSILSEVSTRARSKLPSGKNILVF
GEDGSGKTTLMTKLQGAEHGKKGRGLEYLYLSVHDEDRDDHTRCNVWILDGDLYHKGLLK
FAVSAESLPETLVIFVADMSRPWTVMESLQKWASVLREHIDKMKIPPEKMRELERKFVKD
FQDYMEPEEGCQGSPQRRGPLTSGSDEENVALPLGDNVLTHNLGIPVLVVCTKCDAVSVL
EKEHDYRDEHLDFIQSHLRRFCLQYGAALIYTSVKEEKNLDLLYKYIVHKTYGFHFTTPA
LVVEKDAVFIPAGWDNEKKIAILHENFTTVKPEDAYEDFIVKPPVRKLVHDKELAAEDEQ
VFLMKQQSLLAKQPATPTRASESPARGPSGSPRTQGRGGPASVPSSSPGTSVKKPDPNIK
NNAASEGVLASFFNSLLSKKTGSPGSPGAGGVQSTAKKSGQKTVLSNVQEELDRMTRKPD
SMVTNSSTENEA

Primary citation

Structure of dynein-dynactin on microtubules shows tandem adaptor binding. Chaaban, S., Carter, A.P. Nature (2022) 610:212-216. DOI 10.1038/s41586-022-05186-y · PubMed

Other PDB entries of the same protein (UniProt A0JNT9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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