7Z8L: Cytoplasmic dynein light intermediate chain

Cytoplasmic dynein light intermediate chain (B1) bound to the motor domain (A2). Determined by electron microscopy at 4.9 Å resolution. Released 27 Jul 2022.

Method: Electron microscopy
Resolution: 4.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 16,513
Mol. weight: 589.2 kDa
Ligands: MG, ANP, ATP, ADP
Released: 27 Jul 2022

Explore 7Z8L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z8L contains 184 α-helices and 81 β-strands across 2 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: 170 helices, 73 β-strands

Element	Residues	Length	Sheet
α-helix	1328-1347	20
β-strand	1350	1	1
α-helix	1351-1353	3
α-helix	1356-1370	15
α-helix	1375-1378	4
α-helix	1381-1395	15
α-helix	1397-1403	7
α-helix	1410-1420	11
β-strand	1430	1	1
α-helix	1431-1436	6
α-helix	1443-1472	30
β-strand	1474	1	2
β-strand	1477-1480	4	3
β-strand	1484-1487	4	3
α-helix	1490-1507	18
α-helix	1513-1515	3
α-helix	1517-1551	35
α-helix	1557-1560	4
α-helix	1562-1583	22
β-strand	1587	1	2
α-helix	1588-1592	5
α-helix	1597-1625	29
α-helix	1627-1631	5
α-helix	1634-1642	9
α-helix	1647-1653	7
α-helix	1654-1657	4
β-strand	1663-1666	4	4
β-strand	1672-1677	6	4
β-strand	1683-1691	9	4
α-helix	1698-1728	31
α-helix	1735-1744	10
α-helix	1747-1769	23
α-helix	1776-1797	22
α-helix	1802-1828	27
α-helix	1836-1839	4
β-strand	1843-1846	4	5
β-strand	1857-1861	5	5
β-strand	1864-1867	4	5
α-helix	1876-1878	3
α-helix	1883-1897	15
β-strand	1901-1905	5	6
α-helix	1912-1922	11
α-helix	1925-1926	2
β-strand	1927-1931	5	6
α-helix	1938-1940	3
α-helix	1941-1951	11
β-strand	1954-1958	5	6
α-helix	1960-1962	3
α-helix	1965-1983	19
β-strand	1998-2001	4	7
β-strand	2004-2007	4	7
β-strand	2013-2016	4	6
β-strand	2018	1	6
α-helix	2027-2029	3
β-strand	2036-2040	5	6
α-helix	2046-2056	11
α-helix	2063-2079	17
α-helix	2081-2082	2
α-helix	2090-2117	28
α-helix	2124-2129	6
α-helix	2133-2145	13
α-helix	2146-2148	3
α-helix	2154-2164	11
α-helix	2171-2174	4
α-helix	2176-2188	13
α-helix	2201-2216	16
β-strand	2219-2222	4	8
α-helix	2224-2225	2
α-helix	2230-2245	16
β-strand	2249-2254	6	8
α-helix	2261-2265	5
β-strand	2268	1	9
β-strand	2275	1	9
α-helix	2279-2289	11
β-strand	2298-2304	7	8
α-helix	2310-2312	3
α-helix	2313-2319	7
β-strand	2324-2326	3	10
β-strand	2332-2334	3	10
α-helix	2335-2336	2
β-strand	2339-2344	6	8
α-helix	2353-2358	6
β-strand	2360-2362	3	8
α-helix	2366-2368	3
α-helix	2371-2384	14
α-helix	2396-2399	4
α-helix	2411-2423	13
α-helix	2424-2427	4
α-helix	2432-2442	11
α-helix	2451-2475	25
α-helix	2483-2502	20
α-helix	2503-2505	3
α-helix	2508-2521	14
α-helix	2534-2536	3
β-strand	2537-2539	3	11
α-helix	2540	1
β-strand	2545-2547	3	11
α-helix	2548-2551	4
α-helix	2568-2570	3
α-helix	2572-2586	15
β-strand	2591-2594	4	12
α-helix	2601-2611	11
β-strand	2616-2620	5	12
α-helix	2628-2638	11
β-strand	2639-2643	5	13
β-strand	2648-2652	5	13
β-strand	2659-2663	5	12
α-helix	2670-2671	2
α-helix	2678-2689	12
β-strand	2691-2694	4	13
β-strand	2699-2703	5	13
β-strand	2706-2711	6	12
α-helix	2722-2724	3
α-helix	2725-2728	4
β-strand	2733-2735	3	12
α-helix	2740-2755	16
α-helix	2756-2758	3
α-helix	2763-2765	3
α-helix	2766-2783	18
α-helix	2796-2810	15
α-helix	2818-2829	12
α-helix	2830-2834	5
α-helix	2840-2857	18
α-helix	2863-2866	4
β-strand	2873-2874	2	14
β-strand	2882-2883	2	14
α-helix	2886-2901	16
α-helix	2913-2927	15
β-strand	2933-2936	4	15
α-helix	2946-2953	8
α-helix	2956	1
β-strand	2957-2960	4	15
α-helix	2969-2980	12
α-helix	2981-2985	5
β-strand	2990-2995	6	15
α-helix	3004-3006	3
α-helix	3007-3014	8
α-helix	3024-3040	17
α-helix	3047-3061	15
β-strand	3062-3068	7	15
α-helix	3081-3082	2
α-helix	3083-3088	6
β-strand	3090-3093	4	15
α-helix	3099-3107	9
α-helix	3139-3163	25
α-helix	3166-3168	3
α-helix	3173-3219	47
α-helix	3471-3515	45
α-helix	3522-3538	17
α-helix	3549-3552	4
α-helix	3556-3564	9
α-helix	3571-3579	9
α-helix	3586	1
β-strand	3587-3590	4	16
α-helix	3595-3603	9
α-helix	3605-3607	3
β-strand	3610-3613	4	16
α-helix	3617-3619	3
α-helix	3620-3629	10
β-strand	3633-3636	4	16
α-helix	3638-3640	3
α-helix	3643-3645	3
α-helix	3646-3650	5
β-strand	3654-3656	3	17
β-strand	3659-3664	6	17
β-strand	3667-3670	4	17
β-strand	3677-3681	5	16
α-helix	3690-3694	5
β-strand	3697-3700	4	16
α-helix	3705-3720	16
α-helix	3722-3729	8
α-helix	3736-3751	16
α-helix	3767-3785	19
α-helix	3789-3800	12
α-helix	3802-3817	16
α-helix	3818-3820	3
α-helix	3829-3840	12
α-helix	3844-3846	3
α-helix	3852-3872	21
α-helix	3877-3879	3
α-helix	3880-3894	15
α-helix	3902-3910	9
α-helix	3921-3923	3
α-helix	3929-3938	10
α-helix	3947-3953	7
α-helix	3957-3961	5
α-helix	3966-3969	4
α-helix	3979-3981	3
α-helix	3982-3996	15
α-helix	3998-4000	3
α-helix	4001-4012	12
α-helix	4027-4033	7
β-strand	4041-4045	5	18
α-helix	4052-4062	11
β-strand	4066-4070	5	18
α-helix	4074-4090	17
β-strand	4093-4097	5	18
α-helix	4099-4101	3
α-helix	4103-4113	11
β-strand	4123-4129	7	18
α-helix	4136-4140	5
β-strand	4143-4147	5	18
α-helix	4149-4151	3
α-helix	4153-4163	11
α-helix	4166-4170	5
α-helix	4176-4193	18
α-helix	4194-4196	3
α-helix	4209-4227	19
α-helix	4240-4246	7
α-helix	4247-4251	5
α-helix	4259-4272	14
α-helix	4275-4278	4
β-strand	4283-4288	6	19
β-strand	4292-4295	4	19
α-helix	4296-4297	2
α-helix	4302-4310	9
α-helix	4318-4320	3
α-helix	4326-4344	19
α-helix	4376-4390	15
α-helix	4396-4398	3
α-helix	4402-4405	4
α-helix	4408-4439	32
α-helix	4446-4457	12
α-helix	4459-4461	3
α-helix	4462-4464	3
α-helix	4475-4499	25
α-helix	4500-4502	3
α-helix	4503-4506	4
β-strand	4509-4510	2	20
α-helix	4511-4513	3
α-helix	4517-4532	16
β-strand	4539-4545	7	20
α-helix	4551-4554	4
β-strand	4557-4561	5	20
β-strand	4564-4566	3	21
β-strand	4568-4571	4	21
β-strand	4574-4577	4	21
β-strand	4583-4584	2	21
β-strand	4588-4594	7	20
β-strand	4604-4610	7	21
β-strand	4618-4626	9	21
α-helix	4632-4637	6
β-strand	4641-4643	3	21

Chain q: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	55-60	6	22
α-helix	67-74	8
α-helix	80-82	3
β-strand	86-95	10	22
β-strand	100-109	10	22
α-helix	113-121	9
α-helix	128-130	3
β-strand	131-138	8	22
α-helix	142-144	3
α-helix	145-162	18
α-helix	167-182	16
β-strand	227-232	6	22
α-helix	234-236	3
α-helix	237-243	7
α-helix	248-265	18
β-strand	268-271	4	22
α-helix	280-292	13
β-strand	301	1	22
β-strand	309-310	2	22
α-helix	317-321	5
α-helix	322-326	5
α-helix	336-339	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytoplasmic dynein 1 heavy chain 1	f	protein	4646	Homo sapiens	Q14204
Cytoplasmic dynein 1 light intermediate chain 2	q	protein	492	Homo sapiens	O43237 (AlphaFold model)

Sequence of entity 1 (f), FASTA

>7Z8L_1 Cytoplasmic dynein 1 heavy chain 1 (chains f)
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 2 (q), FASTA

>7Z8L_2 Cytoplasmic dynein 1 light intermediate chain 2 (chains q)
MAPVGVEKKLLLGPNGPAVAAAGDLTSEEEEGQSLWSSILSEVSTRARSKLPSGKNILVF
GEDGSGKTTLMTKLQGAEHGKKGRGLEYLYLSVHDEDRDDHTRCNVWILDGDLYHKGLLK
FAVSAESLPETLVIFVADMSRPWTVMESLQKWASVLREHIDKMKIPPEKMRELERKFVKD
FQDYMEPEEGCQGSPQRRGPLTSGSDEENVALPLGDNVLTHNLGIPVLVVCTKCDAVSVL
EKEHDYRDEHLDFIQSHLRRFCLQYGAALIYTSVKEEKNLDLLYKYIVHKTYGFHFTTPA
LVVEKDAVFIPAGWDNEKKIAILHENFTTVKPEDAYEDFIVKPPVRKLVHDKELAAEDEQ
VFLMKQQSLLAKQPATPTRASESPARGPSGSPRTQGRGGPASVPSSSPGTSVKKPDPNIK
NNAASEGVLASFFNSLLSKKTGSPGSPGAGGVQSTAKKSGQKTVLSNVQEELDRMTRKPD
SMVTNSSTENEA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

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 Q14204), best resolution first:

5OWO 1.79 Å, Human cytoplasmic Dynein N-Terminus dimerization domain at 1.8 Angstrom resolution
9BLZ 2.2 Å, State-1(phi motor) of full-length human dynein-1 in 5mM ATP
9BMR 2.6 Å, State-1 of motor domain from full-length human phi dynein-1 in 5 mM ADP
9DH5 2.6 Å, State-1 of the motor domain from full-length human dynein-1 in 5mM AMPPNP with 5mM Mg2+
9E0X 2.7 Å, Cryo-EM structure of Phi dynein
9E10 2.71 Å, Dimeric motor domains from phi dynein-1 under Lis1 condition
9BM0 2.8 Å, State-2 of motor domain from full-length human dynein-1 in 5mM ATP
9BMF 2.8 Å, State-1(phi motor) of full-length human dynein-1 in 5mM ATPVi
9BMH 2.8 Å, State-4 of motor domain from full-length human dynein-1 in 5mM ATPVi
9BN3 2.8 Å, The alpha registry-locked dynein motor domain mutant in 5mM ATP condition, class1
9BM2 2.82 Å, State-4 of motor domain from full-length human dynein-1 in 5 mM ATP
9BMG 2.86 Å, State-2 of full-length human dynein-1 in 5mM ATPVi

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