6F1U: N terminal region of dynein tail domains

N terminal region of dynein tail domains in complex with dynactin filament and BICDR-1. Determined by electron microscopy at 3.4 Å resolution. Released 17 Jan 2018.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Sus scrofa, Homo sapiens, Mus musculus
Chains: 13
Atoms: 28,866
Mol. weight: 810.94 kDa
Ligands: ADP
Released: 17 Jan 2018

Explore 6F1U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6F1U contains 157 α-helices and 141 β-strands across 13 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: 19 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	1
β-strand	20-25	6	1
β-strand	33-36	4	1
β-strand	39	1	2
β-strand	40	1	3
β-strand	42	1	4
β-strand	45-46	2	5
β-strand	57	1	3
α-helix	60-64	5
β-strand	69	1	4
β-strand	72	1	2
β-strand	75-76	2	6
β-strand	79-80	2	6
α-helix	83-93	11
β-strand	108-111	4	1
α-helix	118-126	9
α-helix	127-132	6
β-strand	136-140	5	1
α-helix	143-150	8
β-strand	155-160	6	7
β-strand	165-171	7	7
β-strand	174-175	2	7
β-strand	181-183	3	7
α-helix	187-201	15
α-helix	211-221	11
β-strand	223	1	8
β-strand	242	1	9
β-strand	248	1	9
α-helix	252-255	4
α-helix	259-263	5
α-helix	275-284	10
α-helix	288-290	3
α-helix	291-295	5
β-strand	298-301	4	7
α-helix	303-306	4
β-strand	308	1	8
α-helix	310-321	12
α-helix	323	1
β-strand	328-331	4	7
α-helix	339-348	10
α-helix	353-356	4
β-strand	358-359	2	1
α-helix	360-365	6
α-helix	368-373	6

Chain c: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
β-strand	19-21	3	5
β-strand	45-47	3	7

Chain d: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	19-21	3	12

Chain D: 20 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	10
β-strand	20-25	6	10
β-strand	33-36	4	10
β-strand	39-42	4	11
β-strand	46	1	12
β-strand	57	1	11
α-helix	61-63	3
α-helix	66-68	3
β-strand	69-72	4	11
β-strand	75-76	2	13
β-strand	79-80	2	13
α-helix	83-93	11
β-strand	108-110	3	10
α-helix	118-126	9
α-helix	127-131	5
β-strand	136-139	4	10
α-helix	144-148	5
β-strand	155-160	6	5
β-strand	165-171	7	5
β-strand	174-175	2	5
α-helix	177-179	3
β-strand	181-183	3	5
α-helix	187-200	14
α-helix	211-221	11
β-strand	223	1	14
β-strand	240-242	3	15
β-strand	248-250	3	15
α-helix	259-261	3
α-helix	275-284	10
α-helix	288-290	3
α-helix	291-295	5
β-strand	298-301	4	5
α-helix	303-306	4
β-strand	308	1	14
α-helix	310-321	12
α-helix	323	1
β-strand	329-331	3	5
α-helix	339-347	9
α-helix	352-356	5
β-strand	358-359	2	10
α-helix	360-365	6
α-helix	368-373	6

Chain f: 29 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	211-222	12
α-helix	233-235	3
α-helix	239-260	22
α-helix	271-293	23
α-helix	295-306	12
α-helix	310-318	9
α-helix	322-332	11
α-helix	342-345	4
α-helix	350-363	14
α-helix	374-397	24
α-helix	406-440	35
α-helix	455-482	28
α-helix	519-533	15
α-helix	539-541	3
α-helix	542	1
α-helix	543-547	5
α-helix	548-574	27
α-helix	578-587	10
α-helix	590-593	4
α-helix	597-603	7
α-helix	605-624	20
α-helix	631-638	8
α-helix	643-669	27
α-helix	679-692	14
α-helix	696-706	11
β-strand	722	1	31
β-strand	726	1	32
β-strand	732	1	32
β-strand	736	1	31
α-helix	742-755	14
α-helix	762-772	11
α-helix	775-796	22
α-helix	801-821	21

Chain F: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	16
β-strand	20-25	6	16
β-strand	33-36	4	16
β-strand	39-42	4	17
α-helix	60-64	5
β-strand	69-72	4	17
β-strand	75-76	2	18
β-strand	79-80	2	18
α-helix	83-93	11
β-strand	108-112	5	16
α-helix	118-126	9
α-helix	127-131	5
β-strand	136-141	6	16
α-helix	142-149	8
β-strand	155-160	6	12
β-strand	165-171	7	12
β-strand	174-175	2	12
α-helix	177-179	3
β-strand	181-183	3	12
α-helix	187-200	14
α-helix	208-220	13
β-strand	223	1	19
α-helix	228-232	5
β-strand	240-242	3	20
α-helix	243	1
β-strand	248-250	3	20
α-helix	254-257	4
α-helix	258-260	3
α-helix	275-284	10
α-helix	291-295	5
β-strand	298-301	4	12
α-helix	303-305	3
β-strand	308	1	19
α-helix	310-321	12
α-helix	323	1
β-strand	329-331	3	12
α-helix	336-338	3
α-helix	339-348	10
α-helix	351-354	4
β-strand	358-359	2	16
α-helix	360-366	7
α-helix	368-373	6

Chain h: 4 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	244-245	2	33
β-strand	259-260	2	34
β-strand	270-271	2	34
β-strand	286-289	4	34
α-helix	292-294	3
β-strand	301-304	4	34
β-strand	311-314	4	35
β-strand	321-325	5	35
β-strand	332-335	4	35
α-helix	346-348	3
β-strand	358-363	6	36
β-strand	372-376	5	36
β-strand	380-384	5	36
β-strand	394-397	4	36
β-strand	399	1	37
β-strand	405	1	37
β-strand	412	1	38
β-strand	421-423	3	38
β-strand	427	1	39
β-strand	430-434	5	38
β-strand	441-446	6	38
β-strand	452	1	39
β-strand	453-457	5	40
β-strand	471-475	5	40
β-strand	479-480	2	41
β-strand	482-483	2	40
β-strand	494-495	2	41
β-strand	504-506	3	42
β-strand	514-516	3	42
β-strand	522-523	2	43
β-strand	524-526	3	42
β-strand	539-540	2	43
β-strand	549-552	4	33
α-helix	553	1
β-strand	559-562	4	33
β-strand	568-571	4	33
α-helix	584-593	10

Chain K: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	11-21	11
α-helix	24-25	2
α-helix	29-40	12
α-helix	43-60	18
β-strand	63-64	2	21
β-strand	75-76	2	21
β-strand	87-89	3	22
α-helix	91-93	3
β-strand	94-96	3	22
β-strand	97-99	3	23
β-strand	104-106	3	23
α-helix	118-135	18
β-strand	136	1	24
β-strand	140-146	7	25
α-helix	148-150	3
β-strand	152-161	10	25
β-strand	164	1	25
α-helix	165-167	3
β-strand	169	1	25
β-strand	172-181	10	25
β-strand	186-191	6	25
β-strand	194-198	5	25
β-strand	203	1	26
β-strand	204-209	6	25
β-strand	211-216	6	25
α-helix	222-248	27
α-helix	250-254	5
α-helix	255-258	4
α-helix	271-276	6

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ARP1 actin related protein 1 homolog A	B, D, F	protein	376	Sus scrofa	F2Z5G5 (AlphaFold model)
Capping protein (Actin filament) muscle Z-line, alpha 1	K	protein	286	Sus scrofa	A0PFK5 (AlphaFold model)
F-actin capping protein beta subunit	L	protein	271	Sus scrofa	A0PFK7 (AlphaFold model)
Dynactin subunit 2	c	protein	50	Sus scrofa	A0A5G2QD80 (AlphaFold model)
Dynactin subunit 2	d	protein	26	Sus scrofa	A0A5G2QD80 (AlphaFold model)
Cytoplasmic dynein 1 heavy chain 1	f, m, n	protein	1186	Homo sapiens	Q14204
Cytoplasmic dynein 1 intermediate chain 2	h	protein	612	Homo sapiens	Q13409
BICD family-like cargo adapter 1	X, x	protein	577	Mus musculus	A0JNT9

Sequence of entity 1 (B, D, F), FASTA

>6F1U_1 ARP1 actin related protein 1 homolog A (chains B, D, F)
MESYDVIANQPVVIDNGSGVIKAGFAGDQIPKYCFPNYVGRPKHVRVMAGALEGDIFIGP
KAEEHRGLLSIRYPMEHGIVKDWNDMERIWQYVYSKDQLQTFSEEHPVLLTEAPLNPRKN
RERAAEVFFETFNVPALFISMQAVLSLYATGRTTGVVLDSGDGVTHAVPIYEGFAMPHSI
MRIDIAGRDVSRFLRLYLRKEGYDFHSSSEFEIVKAIKERACYLSINPQKDETLETEKAQ
YYLPDGSTIEIGPSRFRAPELLFRPDLIGEESEGIHEVLVFAIQKSDMDLRRTLFSNIVL
SGGSTLFKGFGDRLLSEVKKLAPKDVKIRISAPQERLYSTWIGGSILASLDTFKKMWVSK
KEYEEDGARSIHRKTF

Sequence of entity 2 (K), FASTA

>6F1U_2 Capping protein (Actin filament) muscle Z-line, alpha 1 (chains K)
MADFEDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMD
QFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVDGSLKSW
RESCDSALRAYVKDHYSNGFCTVYAKNIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFT
ITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSVTVSNEAQTAKEFIKIIEHAENEYQ
TAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQNA

Sequence of entity 3 (L), FASTA

>6F1U_3 F-actin capping protein beta subunit (chains L)
MSDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYL
LCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVY
LWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTN
KSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIV
NGLRSVQTFADKSKQEALKNDLVEALKRKQQ

Sequence of entity 4 (c), FASTA

>6F1U_4 Dynactin subunit 2 (chains c)
MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDALQEELTSTSVEHIIV

Sequence of entity 5 (d), FASTA

>6F1U_5 Dynactin subunit 2 (chains d)
MADPKYADLPGIARNEPDVYETSDLP

Sequence of entity 6 (f, m, n), FASTA

>6F1U_6 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
EFHSQISKSRQELEQHSVDTASTSDAVTFITYVQSLKRKIKQFEKQ

Sequence of entity 7 (h), FASTA

>6F1U_7 Cytoplasmic dynein 1 intermediate chain 2 (chains h)
MSDKSELKAELERKKQRLAQIREEKKRKEEERKKKETDQKKEAVAPVQEESDLEKKRREA
EALLQSMGLTPESPIVPPPMSPSSKSVSTPSEAGSQDSGDGAVGSRRGPIKLGMAKITQV
DFPPREIVTYTKETQTPVMAQPKEDEEEDDDVVAPKPPIEPEEEKTLKKDEENDSKAPPH
ELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLS
LNRQFFDERWSKHRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPE
YVFHCQSAVMSATFAKFHPNLVVGGTYSGQIVLWDNRSNKRTPVQRTPLSAAAHTHPVYC
VNVVGTQNAHNLISISTDGKICSWSLDMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNN
FVVGSEEGSVYTACRHGSKAGISEMFEGHQGPITGIHCHAAVGAVDFSHLFVTSSFDWTV
KLWSTKNNKPLYSFEDNAGYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDTEVPTASIS
VEGNPALNRVRWTHSGREIAVGDSEGQIVIYDVGEQIAVPRNDEWARFGRTLAEINANRA
DAEEEAATRIPA

Sequence of entity 8 (X, x), FASTA

>6F1U_8 BICD family-like cargo adapter 1 (chains X, x)
MSAFCLGLAGRASAPAEPDSACCMELPAGAGDAVRSPATAAALVSFPGGPGELELALEEE
LALLAAGERSSEPGEHPQAEPESPVEGHGPPLPPPPTQDPELLSVIRQKEKDLVLAARLG
KALLERNQDMSRQYEQMHKELTDKLEHLEQEKHELRRRFENREGEWEGRVSELETDVKQL
QDELERQQLHLREADREKTRAVQELSEQNQRLLDQLSRASEVERQLSMQVHALKEDFREK
NSSTNQHIIRLESLQAEIKMLSDRKRELEHRLSATLEENDLLQGTVEELQDRVLILERQG
HDKDLQLHQSQLELQEVRLSYRQLQGKVEELTEERSLQSSAATSTSLLSEIEQSMEAEEL
EQEREQLRLQLWEAYCQVRYLCSHLRGNDSADSAVSTDSSMDESSETSSAKDVPAGSLRT
ALNDLKRLIQSIVDGVEPTVTLLSVEMTALKEERDRLRVTSEDKEPKEQLQKAIRDRDEA
IAKKNAVELELAKCKMDMMSLNSQLLDAIQQKLNLSQQLEAWQDDMHRVIDRQLMDTHLK
EQSRPAAAAFPRGHGVGRGQEPSTADGKRLFSFFRKI

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3

Primary citation

Cryo-EM shows how dynactin recruits two dyneins for faster movement. Urnavicius, L., Lau, C.K., Elshenawy, M.M. et al. Nature (2018) 554:202-206. DOI 10.1038/nature25462 · PubMed

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

7Z8I 3.3 Å, The barbed end complex of dynactin bound to BICDR1 and the cytoplasmic dynein tails (A2,…
6F1T 3.5 Å, Cryo-EM structure of two dynein tail domains bound to dynactin and BICDR1
6ZNL 3.8 Å, Cryo-EM structure of the dynactin complex
5ADX 4.0 Å, CryoEM structure of dynactin complex at 4.0 angstrom resolution
6ZNM 4.1 Å, The pointed end complex of dynactin bound to BICDR1
7Z8K 4.37 Å, Cytoplasmic dynein (A1) bound to BICDR1
6ZNN 4.5 Å, The pointed end complex of dynactin bound to Hook3
9HHL 6.53 Å, Structure of Dynein-Dynactin-NuMA-LIS1
6F38 6.7 Å, Cryo-EM structure of two dynein tail domains bound to dynactin and HOOK3
6ZNO 6.8 Å, The pointed end complex of dynactin with the p150 projection docked
5AFU 8.2 Å, Cryo-EM structure of dynein tail-dynactin-BICD2N complex
6F3A 8.2 Å, Cryo-EM structure of a single dynein tail domain bound to dynactin and BICD2N

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