5AFU: Dynein tail-dynactin-BICD2N complex

Cryo-EM structure of dynein tail-dynactin-BICD2N complex. Determined by electron microscopy at 8.2 Å resolution. Released 11 Mar 2015.

Method: Electron microscopy
Resolution: 8.2 Å
Organism: SUS SCROFA
Chains: 33
Atoms: 55,952
Mol. weight: 884.75 kDa
Ligands: ADP, ATP
Released: 11 Mar 2015

Explore 5AFU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5AFU contains 331 α-helices and 386 β-strands across 33 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 1: 17 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	9-21	13
α-helix	23-25	3
α-helix	32-50	19
β-strand	63-65	3	1
β-strand	75-77	3	1
α-helix	84-89	6
β-strand	118	1	2
α-helix	126-144	19
α-helix	158-178	21
α-helix	190-197	8
α-helix	217-236	20
α-helix	249-269	21
α-helix	271-273	3
α-helix	275-283	9
α-helix	291-310	20
α-helix	329-344	16
α-helix	346-347	2
α-helix	352-373	22
α-helix	382-409	28
α-helix	419-445	27

Chain 2: 14 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	8-21	14
α-helix	32-50	19
β-strand	63-65	3	7
β-strand	77	1	7
α-helix	83-89	7
β-strand	96-98	3	7
β-strand	116	1	2
β-strand	117-118	2	7
α-helix	126-144	19
α-helix	158-178	21
α-helix	192-198	7
α-helix	217-235	19
α-helix	249-269	21
α-helix	275-283	9
α-helix	292-310	19
α-helix	329-344	16
α-helix	353-373	21
α-helix	382-409	28
α-helix	419-445	27

Chains 3 and 4: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	296-299	4
α-helix	300-303	4
β-strand	315-317	3	8
β-strand	322-325	4	8
β-strand	333-342	10	9
β-strand	349-352	4	10
β-strand	358-363	6	10
β-strand	366-371	6	10
β-strand	377-381	5	10
β-strand	446-451	6	11
β-strand	457-462	6	11
β-strand	467-471	5	11
β-strand	476-481	6	11
β-strand	488-493	6	12
β-strand	499-504	6	12
β-strand	508-513	6	12
β-strand	518-524	7	12
β-strand	529-534	6	13
β-strand	541-546	6	13
β-strand	551-555	5	13
β-strand	561-565	5	13
β-strand	579-584	6	14
β-strand	590-595	6	14
β-strand	600-604	5	14
β-strand	622-626	5	14
β-strand	633-638	6	8
α-helix	640-642	3
β-strand	644-649	6	8
β-strand	653-658	6	8
β-strand	664-669	6	8
β-strand	675-680	6	9
β-strand	691-697	7	9
β-strand	701-709	9	9

Chains 5 and 6: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-274	273

Chains a and b: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	13-15	3	43
α-helix	16-19	4
β-strand	47	1	47
α-helix	52-60	9

Chain A: 21 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	12-14	3	22
β-strand	15	1	23
β-strand	20-23	4	23
β-strand	25	1	22
β-strand	33-36	4	23
β-strand	39-42	4	24
β-strand	45	1	25
β-strand	57	1	24
α-helix	60-64	5
β-strand	69-72	4	24
β-strand	75-76	2	26
β-strand	79-80	2	26
α-helix	83-94	12
β-strand	108-111	4	22
α-helix	118-126	9
α-helix	127-131	5
β-strand	136-140	5	22
α-helix	142-150	9
β-strand	155-160	6	27
β-strand	165-170	6	27
β-strand	175	1	27
β-strand	181-183	3	27
α-helix	187-201	15
α-helix	211-220	10
β-strand	223	1	28
α-helix	228-233	6
α-helix	235-236	2
β-strand	240-242	3	29
β-strand	248-250	3	29
α-helix	254-257	4
α-helix	259-262	4
α-helix	275-285	11
α-helix	288-290	3
α-helix	291-296	6
β-strand	298-299	2	27
α-helix	303-305	3
β-strand	308	1	28
α-helix	310-321	12
α-helix	323	1
β-strand	330-331	2	27
α-helix	339-349	11
α-helix	353-356	4
β-strand	358-359	2	22
α-helix	360-365	6
α-helix	368-375	8

Chain B: 20 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	12-14	3	30
β-strand	15	1	31
β-strand	20-23	4	31
β-strand	25	1	30
β-strand	33-36	4	31
β-strand	39	1	32
β-strand	40	1	33
β-strand	42	1	34
β-strand	45	1	35
β-strand	57	1	33
α-helix	60-64	5
β-strand	69	1	34
β-strand	72	1	32
β-strand	75-76	2	36
β-strand	79-80	2	36
α-helix	83-94	12
β-strand	108-111	4	30
α-helix	118-126	9
α-helix	127-131	5
β-strand	136-140	5	30
α-helix	142-150	9
β-strand	155-159	5	37
β-strand	165-170	6	37
β-strand	175	1	37
β-strand	181-183	3	37
α-helix	187-201	15
α-helix	211-220	10
β-strand	223	1	38
α-helix	228-233	6
α-helix	235-236	2
β-strand	240-242	3	39
β-strand	248-250	3	39
α-helix	254-257	4
α-helix	259-262	4
α-helix	275-285	11
α-helix	291-296	6
β-strand	298-301	4	37
α-helix	303-305	3
β-strand	308	1	38
α-helix	310-321	12
α-helix	323	1
β-strand	328-331	4	37
α-helix	339-349	11
α-helix	353-356	4
β-strand	358-359	2	30
α-helix	360-365	6
α-helix	368-375	8

Chain c: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	13-15	3	35
α-helix	16-19	4
α-helix	41-42	2
β-strand	45-47	3	37

21 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
Dynein tail	1	protein	361	SUS SCROFA
Dynein tail	2	protein	359	SUS SCROFA
Dynein tail	3, 4	protein	350	SUS SCROFA	A0A0J9X2A1 (AlphaFold model)
Dynein tail	5, 6	protein	275	SUS SCROFA
Dynactin	A, B, C, D, E, F, G, I	protein	370	SUS SCROFA	F2Z5G5 (AlphaFold model)
Actin, cytoplasmic 1	H	protein	370	SUS SCROFA	Q6QAQ1 (AlphaFold model)
Dynactin	J	protein	379	SUS SCROFA	I3LHK5 (AlphaFold model)
Capping protein (actin filament) muscle Z-line, alpha 1	K	protein	275	SUS SCROFA	A0PFK5
F-actin capping protein beta subunit variant II	L	protein	270	SUS SCROFA	D2JYW4
Dynactin	M	protein	587	SUS SCROFA
Dynactin 6	N	protein	616	SUS SCROFA
Dynactin	O, P	protein	65	SUS SCROFA

10 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>5AFU_1 DYNEIN TAIL (chains 1)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
X

Sequence of entity 2 (2), FASTA

>5AFU_2 DYNEIN TAIL (chains 2)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 3 (3, 4), FASTA

>5AFU_3 DYNEIN TAIL (chains 3, 4)
HYLVPYNQRANHSKPIPPFLLDLDSQSVPDALKKQTNDYYILYNPALPREIDVELHKSLD
HTSVVCCVKFSNDGEYLATGCNKTTQVYRVSDGSLVARLSDSSDLYIRSVCFSPDGKFLA
TGAEDRLIRIWDIENRKIVMILQGHEQDIYSLDYFPSGDKLVSGSGDRTVRIWDLRTGQC
SLTLSIEDGVTTVAVSPGDGKYIAAGSLDRAVRVWDSETGFLVERLDTGHKDSVYSVVFT
RDGQSVVSGSLDRSVKLWNLTCEVTYIGHKDFVLSVATTQNDEYILSGSKDRGVLFWDKK
SGNPLLMLQGHRNSVISVAVANGSSLGPEYNVFATGSGDCKARIWKYKKI

Sequence of entity 4 (5, 6), FASTA

>5AFU_4 DYNEIN TAIL (chains 5, 6)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 5 (A, B, C, D, E, F, G, I), FASTA

>5AFU_5 DYNACTIN (chains A, B, C, D, E, F, G, I)
IANQPVVIDNGSGVIKAGFAGDQIPKYCFPNYVGRPKHVRVMAGALEGDIFIGPKAEEHR
GLLSIRYPMEHGIVKDWNDMERIWQYVYSKEQLQTFSEEHPVLLTEAPLNPRKNRERAAE
VFFETFNVPALFISMQAVLSLYATGRTTGVVLDSGDGVTHAVPIYEGFAMPHSIMRIDIA
GRDVSRFLRLYLRKEGYDFHSSSEFEIVKAIKERACYLSINPQKDETLETEKAQYYLPDG
STIEIGPSRFRAPELLFRPDLIGEESEGIHEVLVFAIQKSDMDLRRTLFSNIVLSGGSTL
FKGFGDRLLSEVKKLAPKDVKIRISAPQERLYSTWIGGSILASLDTFKKMWVSKKEYEED
GARSIHRKTF

Sequence of entity 6 (H), FASTA

>5AFU_6 ACTIN, CYTOPLASMIC 1 (chains H)
AALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGIL
TLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFE
TFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDL
TDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDG
QVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTM
YPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDES
GPSIVHRKCF

Sequence of entity 7 (J), FASTA

>5AFU_7 DYNACTIN (chains J)
EKTAVVIDLGEAFTKCGFAGETGPRCIIPSVIKKAGMPKPIKVVQYNINTEELYSYLKEF
IHILYFRHLLVNPRDRRVVVIESVLCPSHFRETLTRVLFKYFEVPSVLLAPSHLMALLTL
GINSAMVLDCGYRESLVLPIYEGIPVLNCWGALPLGGKALHKELETQLLEQCTVDTGAAK
EQSLPSVMGSIPEGVLEDIKVRTCFVSDLTRGLKIQAAKFNIDGNTERPSPPPNVDYPLD
GEKILHVLGSIRDSVVEILFEQDNEEKSVATLILDSLMQCPIDTRKQLAENLVIIGGTSM
LPGFLHRLLAEIRYLVEKPKYKKTLGTKTFRIHTPPAKANCVAWLGGAIFGALQDILGSR
SVSKEYYNQTGRIPDWCSL

Sequence of entity 8 (K), FASTA

>5AFU_8 CAPPING PROTEIN (ACTIN FILAMENT) MUSCLE Z-LINE, ALPHA 1 (chains K)
RVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVK
IEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVDGSLKSWRESCDS
ALRAYVKDHYSNGFCTVYAKNIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTA
QVVGVLKIQVHYYEDGNVQLVSHKDVQDSVTVSNEAQTAKEFIKIIEHAENEYQTAISEN
YQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGK

Sequence of entity 9 (L), FASTA

>5AFU_9 F-ACTIN CAPPING PROTEIN BETA SUBUNIT VARIANT II (chains L)
SDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYLL
CDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVYL
WDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTNK
SGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIVN
GLRSVDVIPDNPKFQQLQRELSQVLTQRQI

Sequence of entity 10 (M), FASTA

>5AFU_10 DYNACTIN (chains M)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 11 (N), FASTA

>5AFU_11 DYNACTIN 6 (chains N)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXX

Sequence of entity 12 (O, P), FASTA

>5AFU_12 DYNACTIN (chains O, P)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXX

Ligands and cofactors

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

Primary citation

The Structure of the Dynactin Complex and its Interaction with Dynein. Urnavicius, L., Zhang, K., Diamant, A.G. et al. Science (2015) 347:1441. DOI 10.1126/SCIENCE.AAA4080 · PubMed

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