8PR3: Cytoplasmic dynein-1 heavy chain

Cytoplasmic dynein-1 heavy chain bound to JIP3-RH1. Determined by electron microscopy at 3.9 Å resolution. Released 27 Mar 2024.

Method
Electron microscopy
Resolution
3.9 Å
Organism
Homo sapiens
Chains
9
Atoms
17,888
Mol. weight
1497.46 kDa
Released
27 Mar 2024

Explore 8PR3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PR3 contains 78 α-helices and 82 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 B: 2 helices, 0 β-strands

ElementResiduesLengthSheet
α-helix27-4620
α-helix56-12772
Chain C: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix24-263
α-helix27-4620
α-helix56-12772
Chains E and F: 1 helix, 0 β-strands
ElementResiduesLengthSheet
α-helix430-4389
Chain f: 23 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix561-57111
α-helix578-5858
α-helix589-5913
α-helix597-6037
α-helix605-62420
α-helix631-6366
α-helix643-66927
α-helix677-69014
α-helix691-6933
α-helix696-70914
β-strand71611
β-strand718-72362
β-strand732-73762
α-helix741-75313
α-helix762-77211
α-helix775-79723
α-helix799-8057
α-helix806-81914
β-strand82311
α-helix829-86234
α-helix871-89020
α-helix896-92227
α-helix986-9949
α-helix9961
β-strand99713
α-helix998-10003
α-helix1014-10174
β-strand101813
α-helix1031-10388
Chain h: 5 helices, 30 β-strands
ElementResiduesLengthSheet
β-strand239-24574
β-strand256-26165
β-strand268-27365
β-strand285-29175
β-strand301-30555
β-strand309-31466
β-strand321-32666
β-strand331-33556
β-strand34516
α-helix3571
β-strand358-36587
β-strand370-37677
β-strand380-38457
β-strand394-39747
β-strand39918
β-strand40518
β-strand408-41259
β-strand420-42569
β-strand430-43459
β-strand441-44669
β-strand453-458610
β-strand470-475610
β-strand480-484510
β-strand492-494310
β-strand501-506611
β-strand513-518611
β-strand522-527611
β-strand537-540411
β-strand550-55234
β-strand558-56144
β-strand568-57364
α-helix5741
α-helix575-5784
α-helix580-5812
α-helix584-60724
Chain j: 15 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix50-523
β-strand56-60512
α-helix67-759
β-strand86-94912
β-strand101-109912
α-helix113-1186
α-helix119-1224
β-strand131-138812
α-helix142-1443
α-helix145-16016
α-helix169-18214
β-strand227-232612
α-helix234-2374
α-helix238-2425
α-helix248-26518
β-strand269-271312
β-strand273113
β-strand278113
α-helix280-29213
β-strand301112
β-strand309-310212
α-helix321-3244
α-helix342-3443
α-helix356-3583
α-helix359-37214
Chain m: 25 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix271-28616
α-helix323-33614
α-helix341-3466
α-helix350-36314
α-helix374-39926
α-helix401-4033
α-helix406-43833
α-helix457-48327
α-helix514-53118
α-helix540-56829
α-helix571-5744
α-helix578-58710
α-helix589-5935
α-helix595-6006
α-helix603-62220
α-helix631-6377
α-helix643-66927
α-helix673-6753
α-helix679-69214
α-helix696-70914
β-strand716114
β-strand719115
β-strand736115
α-helix743-75311
α-helix762-79736
α-helix799-8013
α-helix806-82015
β-strand823114
α-helix829-85325
Chain o: 3 helices, 32 β-strands
ElementResiduesLengthSheet
β-strand239-245716
β-strand256-261617
β-strand268-273617
β-strand285-291717
β-strand301-305517
β-strand309-314618
β-strand321-326618
β-strand331-335518
β-strand345118
β-strand358-365819
β-strand370-376719
β-strand380-384519
β-strand385120
β-strand388120
β-strand395-397319
β-strand399-400221
β-strand404-405221
α-helix4061
β-strand411-412222
β-strand420-423422
β-strand430-434522
β-strand441-446622
β-strand453-458623
β-strand470-475623
β-strand480-484523
β-strand492-494323
β-strand501-506624
β-strand513-518624
β-strand522-527624
β-strand537-540424
β-strand547-552616
β-strand558-563616
β-strand568-573616
α-helix575-5784
α-helix584-60724

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
C-Jun-amino-terminal kinase-interacting protein 3B, Cprotein581Homo sapiensQ9UPT6 (AlphaFold model)
Cytoplasmic dynein 1 heavy chain 1f, mprotein4646Homo sapiensQ14204
Cytoplasmic dynein 1 intermediate chain 2h, oprotein612Homo sapiensQ13409 (AlphaFold model)
Cytoplasmic dynein 1 light intermediate chain 2E, F, jprotein492Homo sapiensO43237 (AlphaFold model)
Sequence of entity 1 (B, C), FASTA
>8PR3_1 C-Jun-amino-terminal kinase-interacting protein 3 (chains B, C)
SNIEFLKMMEIQMDEGGGVVVYQDDYCSGSVMSERVSGLAGSIYREFERLIHCYDEEVVK
ELMPLVVNVLENLDSVLSENQEHEVELELLREDNEQLLTQYEREKALRRQAEEKFIEFED
ALEQEKKELQIQVEHYEFQTRQLELKAKNYADQISRLEERESEMKKEYNALHQRHTEMIQ
TYVEHIERSKMQQVGGNSQTESSLPGRRKERPTSLNVFPLADGTVRAQIGGKLVPAGDHW
HLSDLGQLQSSSSYQCPQDEMSESGQSSAAATPSTTGTKSNTPTSSVPSAAVTPLNESLQ
PLGDYGVGSKNSKRAREKRDSRNMEVQVTQEMRNVSIGMGSSDEWSDVQDIIDSTPELDM
CPETRLDRTGSSPTQGIVNKAFGINTDSLYHELSTAGSEVIGDVDEGADLLGEFSVRDDF
FGMGKEVGNLLLENSQLLETKNALNVVKNDLIAKVDQLSGEQEVLRGELEAAKQAKVKLE
NRIKELEEELKRVKSEAIIARREPKEEAEDVSSYLCTESDKIPMAQRRRFTRVEMARVLM
ERNQYKERLMELQEAVRWTEMIRASREGSGSGRWSHPQFEK
Sequence of entity 2 (f, m), FASTA
>8PR3_2 Cytoplasmic dynein 1 heavy chain 1 (chains f, m)
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
LPVETQEFQSISTEFLALMKKVSKSPLVMDVLNIQGVQRSLERLADLLGEIQKALGEYLE
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
>8PR3_3 Cytoplasmic dynein 1 intermediate chain 2 (chains h, o)
MSDKSELKAELERKKQRLAQIREEKKRKEEERKKKETDQKKEAVAPVQEESDLEKKRREA
EALLQSMGLTPESPIVPPPMSPSSKSVSTPSEAGSQDSGDGAVGSRRGPIKLGMAKITQV
DFPPREIVTYTKETQTPVMAQPKEDEEEDDDVVAPKPPIEPEEEKTLKKDEENDSKAPPH
ELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLS
LNRQFFDERWSKHRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPE
YVFHCQSAVMSATFAKFHPNLVVGGTYSGQIVLWDNRSNKRTPVQRTPLSAAAHTHPVYC
VNVVGTQNAHNLISISTDGKICSWSLDMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNN
FVVGSEEGSVYTACRHGSKAGISEMFEGHQGPITGIHCHAAVGAVDFSHLFVTSSFDWTV
KLWSTKNNKPLYSFEDNAGYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDTEVPTASIS
VEGNPALNRVRWTHSGREIAVGDSEGQIVIYDVGEQIAVPRNDEWARFGRTLAEINANRA
DAEEEAATRIPA
Sequence of entity 4 (E, F, j), FASTA
>8PR3_4 Cytoplasmic dynein 1 light intermediate chain 2 (chains E, F, j)
MAPVGVEKKLLLGPNGPAVAAAGDLTSEEEEGQSLWSSILSEVSTRARSKLPSGKNILVF
GEDGSGKTTLMTKLQGAEHGKKGRGLEYLYLSVHDEDRDDHTRCNVWILDGDLYHKGLLK
FAVSAESLPETLVIFVADMSRPWTVMESLQKWASVLREHIDKMKIPPEKMRELERKFVKD
FQDYMEPEEGCQGSPQRRGPLTSGSDEENVALPLGDNVLTHNLGIPVLVVCTKCDAVSVL
EKEHDYRDEHLDFIQSHLRRFCLQYGAALIYTSVKEEKNLDLLYKYIVHKTYGFHFTTPA
LVVEKDAVFIPAGWDNEKKIAILHENFTTVKPEDAYEDFIVKPPVRKLVHDKELAAEDEQ
VFLMKQQSLLAKQPATPTRASESPARGPSGSPRTQGRGGPASVPSSSPGTSVKKPDPNIK
NNAASEGVLASFFNSLLSKKTGSPGSPGAGGVQSTAKKSGQKTVLSNVQEELDRMTRKPD
SMVTNSSTENEA

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 Q9UPT6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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