6F38: Two dynein tail domains

Cryo-EM structure of two dynein tail domains bound to dynactin and HOOK3. Determined by electron microscopy at 6.7 Å resolution. Released 17 Jan 2018.

Method: Electron microscopy
Resolution: 6.7 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 45
Atoms: 68,864
Mol. weight: 1967.09 kDa
Ligands: ATP, ADP
Released: 17 Jan 2018

Explore 6F38 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6F38 contains 521 α-helices and 476 β-strands across 45 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: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	18	1	51
α-helix	52-58	7

Chain A: 19 helices, 20 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	39-40	2	2
β-strand	57	1	2
α-helix	66-68	3
β-strand	71-72	2	2
β-strand	75-76	2	3
β-strand	79-80	2	3
α-helix	83-94	12
α-helix	103-105	3
β-strand	107-111	5	1
α-helix	118-126	9
α-helix	127-131	5
β-strand	136-140	5	1
α-helix	144-150	7
β-strand	154-160	7	4
β-strand	165-171	7	4
β-strand	174-175	2	4
β-strand	181-183	3	4
α-helix	187-199	13
α-helix	208-218	11
β-strand	223	1	5
α-helix	230-233	4
β-strand	241-242	2	6
β-strand	248-249	2	6
α-helix	253-255	3
α-helix	257-261	5
α-helix	265-268	4
α-helix	275-284	10
α-helix	289-295	7
β-strand	298-302	5	4
α-helix	303-305	3
β-strand	308	1	5
α-helix	310-321	12
β-strand	330-331	2	4
α-helix	336-348	13
α-helix	360-366	7
α-helix	368-373	6

Chain b: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	19	1	94
α-helix	52-58	7
β-strand	65	1	166
β-strand	85	1	166

Chain B: 19 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	7
β-strand	16	1	8
β-strand	20-23	4	8
β-strand	24-25	2	7
β-strand	33-36	4	8
β-strand	39	1	9
β-strand	40	1	10
β-strand	57	1	10
α-helix	60-64	5
β-strand	72	1	9
β-strand	75-76	2	11
β-strand	79-80	2	11
α-helix	83-93	11
β-strand	108	1	12
β-strand	109	1	7
β-strand	112	1	13
α-helix	118-126	9
α-helix	127-131	5
β-strand	136	1	14
β-strand	137	1	12
β-strand	141	1	13
α-helix	142-150	9
β-strand	155-158	4	15
β-strand	165-170	6	15
β-strand	175	1	15
β-strand	181-183	3	15
α-helix	187-200	14
α-helix	208-220	13
α-helix	228-231	4
β-strand	241-242	2	16
β-strand	248-249	2	16
α-helix	252-255	4
α-helix	258-263	6
α-helix	265-268	4
α-helix	275-284	10
α-helix	290-296	7
β-strand	298-300	3	15
α-helix	303-305	3
α-helix	310-320	11
β-strand	328-330	3	17
β-strand	331	1	15
α-helix	336-348	13
α-helix	353-356	4
β-strand	359	1	14
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	33
β-strand	45-47	3	17

Chain C: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	20
β-strand	20-25	6	20
β-strand	33-36	4	20
β-strand	39-42	4	21
β-strand	45-46	2	22
β-strand	69-72	4	21
β-strand	75-76	2	23
β-strand	79-80	2	23
α-helix	83-93	11
α-helix	103-105	3
β-strand	108-111	4	20
α-helix	118-126	9
α-helix	127-131	5
β-strand	137-140	4	20
α-helix	142-150	9
β-strand	155-158	4	24
β-strand	165-170	6	24
α-helix	177-179	3
β-strand	181-183	3	24
α-helix	187-200	14
α-helix	208-220	13
α-helix	228-232	5
β-strand	240-241	2	25
β-strand	249-250	2	25
α-helix	254-260	7
α-helix	261-263	3
α-helix	274-284	11
α-helix	290-296	7
β-strand	297	1	26
β-strand	298-300	3	24
α-helix	303-305	3
α-helix	310-320	11
β-strand	329	1	26
α-helix	336-348	13
α-helix	353-356	4
α-helix	360-364	5
α-helix	368-375	8

Chain d: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4

Chain D: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	28
β-strand	20-25	6	28
β-strand	33-36	4	28
β-strand	40	1	29
β-strand	57	1	29
α-helix	59-62	4
β-strand	71	1	29
β-strand	75-76	2	30
β-strand	79-80	2	30
α-helix	83-93	11
β-strand	108-112	5	28
α-helix	118-130	13
β-strand	137-141	5	28
α-helix	142-150	9
β-strand	155-160	6	31
β-strand	165-171	7	31
β-strand	174-175	2	31
α-helix	177-179	3
β-strand	181-183	3	31
α-helix	187-200	14
α-helix	208-220	13
β-strand	240-242	3	32
β-strand	248-250	3	32
α-helix	254-257	4
α-helix	258-262	5
α-helix	265-267	3
α-helix	275-284	10
α-helix	290-296	7
β-strand	298-300	3	31
α-helix	310-320	11
β-strand	329-331	3	33
α-helix	338-348	11
α-helix	360-365	6
α-helix	368-375	8

37 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	A, B, C, D, E, F, G, I	protein	376	Sus scrofa	F2Z5G5 (AlphaFold model)
Actin, cytoplasmic 1	H	protein	375	Sus scrofa	Q6QAQ1 (AlphaFold model)
Actin related protein 10 homolog	J	protein	390	Sus scrofa	I3LHK5 (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	272	Sus scrofa	A0PFK7
Dynactin Subunit 2	M	protein	587	Sus scrofa
Dynactin Subunit 2	N	protein	616	Sus scrofa
Dynactin Subunit 3	O, P	protein	65	Sus scrofa
Dynactin Subunit 2	Q, R	protein	87	Sus scrofa
Dynactin 6	U	protein	190	Sus scrofa	D0G6S1
Dynactin subunit 5	V	protein	182	Sus scrofa	A0A286ZK88
HOOK3	X, x	protein	223	Homo sapiens

11 more molecules are not listed.

Sequence of entity 1 (A, B, C, D, E, F, G, I), FASTA

>6F38_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

>6F38_2 Actin, cytoplasmic 1 (chains H)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF

Sequence of entity 3 (J), FASTA

>6F38_3 Actin related protein 10 homolog (chains J)
MPLYEGLGSGGEKTAVVIDLGEAFTKCGFAGETGPRCIIPSVIKKAGMPKPIKVVQYNIN
TEELYSYLKEFIHILYFRHLLVNPRDRRVVVIESVLCPSHFRETLTRVLFKYFEVPSVLL
APSHLMALLTLGINSAMVLDCGYRESLVLPIYEGIPVLNCWGALPLGGKALHKELETQLL
EQCTVDTGAAKEQSLPSVMGSIPEGVLEDIKVRTCFVSDLTRGLKIQAAKFNIDGNTERP
SPPPNVDYPLDGEKILHVLGSIRDSVVEILFEQDNEEKSVATLILDSLMQCPIDTRKQLA
ENLVIIGGTSMLPGFLHRLLAEIRYLVEKPKYKKTLGTKTFRIHTPPAKANCVAWLGGAI
FGALQDILGSRSVSKEYYNQTGRIPDWCSL

Sequence of entity 4 (K), FASTA

>6F38_4 Capping protein (Actin filament) muscle Z-line, alpha 1 (chains K)
MADFEDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMD
QFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVDGSLKSW
RESCDSALRAYVKDHYSNGFCTVYAKNIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFT
ITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSVTVSNEAQTAKEFIKIIEHAENEYQ
TAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQNA

Sequence of entity 5 (L), FASTA

>6F38_5 F-actin capping protein beta subunit (chains L)
MSDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYL
LCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVY
LWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTN
KSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIV
NGLRSVQTFADKSKQEALKNDLVEALKRKQQC

Sequence of entity 6 (M), FASTA

>6F38_6 Dynactin Subunit 2 (chains M)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 7 (N), FASTA

>6F38_7 Dynactin Subunit 2 (chains N)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXX

Sequence of entity 8 (O, P), FASTA

>6F38_8 Dynactin Subunit 3 (chains O, P)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXX

Sequence of entity 9 (Q, R), FASTA

>6F38_9 Dynactin Subunit 2 (chains Q, R)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 10 (U), FASTA

>6F38_10 Dynactin 6 (chains U)
MAEKTQKSVKIAPGAVVCVESEIRGDVTIGPRTVIHPKARIIAEAGPIVIGEGNLIEEQA
LIINAHPDNITPDAEDSEPKPMIIGTNNVFEVGCYSQAMKMGDNNVIESKAYVGRNVILT
SGCIIGACCNLNTFEVIPENTVIYGADCLRRVQTERPQPQTLQLDFLMKILPNYHHLKKT
MKGSSTPVKN

Sequence of entity 11 (V), FASTA

>6F38_11 Dynactin subunit 5 (chains V)
MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTIVMNDCIIRGDLANVRVGRH
CVVKSRSVIRPPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRC
VLKDCCKILDNTVLPPETVVPPFTVFSGCPGLFSGELPECTQELMIDVTKSYYQKFLPLT
QV

Sequence of entity 12 (X, x), FASTA

>6F38_12 HOOK3 (chains X, x)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	9

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,…
6F1U 3.4 Å, N terminal region of dynein tail domains in complex with dynactin filament and BICDR-1
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
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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