6ZO4: The pointed end complex of dynactin

The pointed end complex of dynactin bound to BICD2. Determined by electron microscopy at 8.2 Å resolution. Released 29 Jul 2020.

Method: Electron microscopy
Resolution: 8.2 Å
Organisms: Mus musculus, Sus scrofa
Chains: 10
Atoms: 19,302
Mol. weight: 338.56 kDa
Ligands: ADP, ATP, ZN
Released: 29 Jul 2020

Explore 6ZO4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZO4 contains 122 α-helices and 158 β-strands across 10 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.

Chains 5 and 6: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	132-274	143

Chain G: 26 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
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	41-42	2	3
β-strand	45	1	4
α-helix	46	1
α-helix	52-53	2
β-strand	57-58	2	2
α-helix	60-64	5
β-strand	69-70	2	3
α-helix	71	1
β-strand	75-76	2	5
β-strand	79-80	2	5
α-helix	83-94	12
β-strand	108-111	4	1
α-helix	112-113	2
α-helix	118-130	13
β-strand	136-140	5	1
α-helix	142-150	9
β-strand	155-160	6	6
β-strand	165-171	7	6
β-strand	174-175	2	6
α-helix	177-179	3
β-strand	181-183	3	6
α-helix	187-201	15
α-helix	210-220	11
β-strand	223	1	7
α-helix	228-233	6
α-helix	235-237	3
β-strand	240-242	3	8
β-strand	248-250	3	8
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	298-301	4	6
α-helix	303-305	3
β-strand	308	1	7
α-helix	310-321	12
α-helix	323	1
β-strand	330-333	4	6
α-helix	339-349	11
α-helix	353-356	4
β-strand	358-359	2	1
α-helix	360-366	7
α-helix	368-374	7

Chain H: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	9
β-strand	16-21	6	9
β-strand	29-32	4	9
β-strand	35-38	4	10
α-helix	44-45	2
β-strand	53-54	2	10
α-helix	56-60	5
β-strand	65-68	4	10
β-strand	71-72	2	11
β-strand	75-76	2	11
α-helix	79-87	9
α-helix	88-94	7
β-strand	103-107	5	9
α-helix	113-125	13
β-strand	131-136	6	9
α-helix	137-143	7
β-strand	150-155	6	12
β-strand	160-166	7	12
β-strand	169-170	2	12
α-helix	172-174	3
β-strand	176-178	3	12
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-232	10
β-strand	239-241	3	13
β-strand	247-249	3	13
α-helix	253-256	4
α-helix	259-262	4
α-helix	264-266	3
α-helix	274-284	11
α-helix	290-295	6
β-strand	297-298	2	12
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	12
α-helix	338-348	11
α-helix	350-354	5
α-helix	356	1
β-strand	357-358	2	9
α-helix	359-365	7
α-helix	369-372	4

Chain I: 20 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
β-strand	12-15	4	14
β-strand	20-25	6	14
β-strand	33-36	4	14
β-strand	39-42	4	15
β-strand	57-58	2	15
α-helix	60-64	5
β-strand	69-72	4	15
β-strand	75-76	2	16
β-strand	79-80	2	16
α-helix	83-93	11
β-strand	95	1	17
β-strand	99	1	17
β-strand	108-112	5	14
α-helix	113	1
α-helix	118-130	13
β-strand	136-141	6	14
α-helix	142-150	9
β-strand	155-160	6	4
β-strand	165-170	6	4
β-strand	175	1	4
β-strand	181-183	3	4
α-helix	187-201	15
α-helix	210-220	11
β-strand	223	1	18
α-helix	228-233	6
α-helix	235-236	2
β-strand	240-242	3	19
β-strand	248-250	3	19
α-helix	254-257	4
α-helix	259-262	4
α-helix	275-285	11
α-helix	288-295	8
β-strand	298-301	4	4
β-strand	308	1	18
α-helix	310-321	12
α-helix	323	1
β-strand	329-331	3	4
α-helix	339-349	11
α-helix	353-356	4
β-strand	358-359	2	14
α-helix	360-366	7
α-helix	370-374	5

Chain J: 23 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	16-19	4	20
β-strand	24-29	6	20
β-strand	37-40	4	20
β-strand	42-43	2	21
α-helix	51	1
β-strand	52-53	2	21
α-helix	61-74	14
α-helix	75-79	5
β-strand	89-92	4	20
α-helix	99-108	10
α-helix	109-113	5
β-strand	117-121	5	20
α-helix	123-131	9
β-strand	136-141	6	22
β-strand	146-152	7	22
β-strand	155-156	2	22
α-helix	158-160	3
β-strand	162-164	3	22
α-helix	168-181	14
β-strand	185-186	2	23
β-strand	195	1	23
α-helix	204-213	10
α-helix	217-219	3
α-helix	220-231	12
α-helix	240-245	6
β-strand	246-250	5	23
β-strand	254-258	5	23
α-helix	260-265	6
α-helix	268-271	4
α-helix	280-290	11
α-helix	296-301	6
β-strand	303-306	4	22
α-helix	308-311	4
α-helix	315-328	14
α-helix	330-333	4
β-strand	343	1	22
α-helix	350-352	3
α-helix	354-362	9
α-helix	365-371	7
β-strand	373-374	2	20
α-helix	375-381	7

Chain M: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	19-21	3	4
β-strand	46-48	3	6
α-helix	52-59	8

Chain U: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	23-25	3	24
β-strand	28	1	25
β-strand	35	1	26
α-helix	36	1
β-strand	41-43	3	24
β-strand	48-49	2	25
β-strand	56	1	26
β-strand	62	1	24
α-helix	66-69	4
β-strand	82-83	2	25
β-strand	88-90	3	26
β-strand	96	1	24
β-strand	100	1	25
β-strand	105-107	3	26
β-strand	112	1	27
β-strand	123	1	26
α-helix	125-126	2
β-strand	130	1	27
α-helix	136-138	3
β-strand	141-143	3	28
β-strand	151-153	3	28
α-helix	157-159	3
α-helix	162-170	9

Chain V: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	29
α-helix	5-7	3
β-strand	8-10	3	30
β-strand	15-17	3	31
β-strand	20-22	3	31
β-strand	35-36	2	32
β-strand	41-42	2	31
β-strand	47	1	33
β-strand	56-57	2	32
β-strand	62-63	2	31
β-strand	68-69	2	33
α-helix	71-72	2
β-strand	73-74	2	34
β-strand	81-82	2	34
α-helix	83-85	3
β-strand	86	1	32
β-strand	87	1	35
β-strand	92-93	2	31
β-strand	98-99	2	33
β-strand	104	1	35
α-helix	105	1
β-strand	109-110	2	31
β-strand	115-116	2	33
β-strand	121-122	2	35
β-strand	127-128	2	31
α-helix	129	1
β-strand	133-134	2	33
β-strand	139-140	2	35
β-strand	145-147	3	31
β-strand	152-155	4	31
α-helix	162-175	14
β-strand	176-178	3	30

1 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
BICD2	5, 6	protein	145	Mus musculus
ARP1 actin related protein 1 homolog A	G, I	protein	376	Sus scrofa	F2Z5G5 (AlphaFold model)
Actin, cytoplasmic 1	H	protein	375	Sus scrofa	Q6QAQ1 (AlphaFold model)
Arp11	J	protein	417	Sus scrofa	I3LHK5 (AlphaFold model)
Dynactin subunit 2	M	protein	405	Sus scrofa	A0A5G2QD80 (AlphaFold model)
Dynactin 6	U	protein	190	Sus scrofa	D0G6S1
Dynactin subunit 5	V	protein	182	Sus scrofa	A0A286ZK88
Dynactin subunit 4	Y	protein	467	Sus scrofa	A0A4X1TB62

Sequence of entity 1 (5, 6), FASTA

>6ZO4_1 BICD2 (chains 5, 6)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 2 (G, I), FASTA

>6ZO4_2 ARP1 actin related protein 1 homolog A (chains G, I)
MESYDVIANQPVVIDNGSGVIKAGFAGDQIPKYCFPNYVGRPKHVRVMAGALEGDIFIGP
KAEEHRGLLSIRYPMEHGIVKDWNDMERIWQYVYSKDQLQTFSEEHPVLLTEAPLNPRKN
RERAAEVFFETFNVPALFISMQAVLSLYATGRTTGVVLDSGDGVTHAVPIYEGFAMPHSI
MRIDIAGRDVSRFLRLYLRKEGYDFHSSSEFEIVKAIKERACYLSINPQKDETLETEKAQ
YYLPDGSTIEIGPSRFRAPELLFRPDLIGEESEGIHEVLVFAIQKSDMDLRRTLFSNIVL
SGGSTLFKGFGDRLLSEVKKLAPKDVKIRISAPQERLYSTWIGGSILASLDTFKKMWVSK
KEYEEDGARSIHRKTF

Sequence of entity 3 (H), FASTA

>6ZO4_3 Actin, cytoplasmic 1 (chains H)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF

Sequence of entity 4 (J), FASTA

>6ZO4_4 Arp11 (chains J)
MPLYEGLGSGGEKTAVVIDLGEAFTKCGFAGETGPRCIIPSVIKKAGMPKPIKVVQYNIN
TEELYSYLKEFIHILYFRHLLVNPRDRRVVVIESVLCPSHFRETLTRVLFKYFEVPSVLL
APSHLMALLTLGINSAMVLDCGYRESLVLPIYEGIPVLNCWGALPLGGKALHKELETQLL
EQCTVDTGAAKEQSLPSVMGSIPEGVLEDIKVRTCFVSDLTRGLKIQAAKFNIDGNTERP
SPPPNVDYPLDGEKILHVLGSIRDSVVEILFEQDNEEKSVATLILDSLMQCPIDTRKQLA
ENLVIIGGTSMLPGFLHRLLAEIRYLVEKPKYKKTLGTKTFRIHTPPAKANCVAWLGGAI
FGALQDILGSRSVSKEYYNQTGRIPDWCSLNNPPLEMVFDVGKSQPPLMKRAFSTEK

Sequence of entity 5 (M), FASTA

>6ZO4_5 Dynactin subunit 2 (chains M)
MADPKYADLPGIARNEPDVYETSDLPEDDQAEFDAELEELTSTSVEHIIVNPNAAYDKFK
DKRVGTKGLDFSDRIGKTKRTGYESGEYEMLGEGLGVKETPQQKYQRLLHEVQELTTEVE
KIKMTVKESATEEKLTPVVLAKQLAALKQQLVASHLEKLLGPDAAINLTDPDGALAKRLL
LQLEATKNTKGAGSGGKTTSGSPPDSSLVTYELHSRPEQDKFSQAAKVAELEKRLTELEA
TVRCDQDAQNPLSAGLQGACLMETVELLQAKVSALDLAVLDQVEARLQSVLGKVNEIAKH
KASVEDADTQSKVHQLYETIQRWSPIASTLPELVQRLVTIKQLHEQAMQFGQLLTHLDTT
QQMIACSLKDNATLLTQVQTTMRENLSTVEGNFANIDERMKKLGK

Sequence of entity 6 (U), FASTA

>6ZO4_6 Dynactin 6 (chains U)
MAEKTQKSVKIAPGAVVCVESEIRGDVTIGPRTVIHPKARIIAEAGPIVIGEGNLIEEQA
LIINAHPDNITPDAEDSEPKPMIIGTNNVFEVGCYSQAMKMGDNNVIESKAYVGRNVILT
SGCIIGACCNLNTFEVIPENTVIYGADCLRRVQTERPQPQTLQLDFLMKILPNYHHLKKT
MKGSSTPVKN

Sequence of entity 7 (V), FASTA

>6ZO4_7 Dynactin subunit 5 (chains V)
MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTIVMNDCIIRGDLANVRVGRH
CVVKSRSVIRPPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRC
VLKDCCKILDNTVLPPETVVPPFTVFSGCPGLFSGELPECTQELMIDVTKSYYQKFLPLT
QV

Sequence of entity 8 (Y), FASTA

>6ZO4_8 Dynactin subunit 4 (chains Y)
MASLLQSERVLYLVQGEKKVRAPLSQLYFCRYCSELRSLECVSHEVDSHYCPSCLENMPS
AEAKLKKNRCANCFDCPGCMHTLSTRATSISTQLPDDPAKTAVKKAYYLACGFCRWTSRD
VGMADKSVASGGWQEPDHPHTQRMNKLIEYYQQLAQKEKVERDRKKLARRRNYMPLAFSQ
HTIHVVDKYGLGTRLQRPRAGTTITALAGLSLKEGEDQKEIKIEPAQAVDEVEPLPEDYY
TRPVNLTEVTTLQQRLLQPDFQPICASQLYPRHKHLLIKRSLRCRQCEHNLSKPEFNPTS
IKFKIQLVAVNYIPEVRIMSIPNLRYMKESQVLLTLTNPVENLTHVTLLECEEGDPDDTN
STAKVSVPPTELVLAGKDAAAEYDELAEPQDFPDDPDVVAFRKANKVGVFIKVTPQREEG
DVTVCFKLKHDFKNLAAPIRPVEEADPGAEVSWLTQHVELSLGPLLP

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
ZN	Zinc ion	Zn	3

Primary citation

Cryo-EM reveals the complex architecture of dynactin's shoulder region and pointed end. Lau, C.K., O'Reilly, F.J., Santhanam, B. et al. EMBO J (2021) 40:e106164-e106164. DOI 10.15252/embj.2020106164 · 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
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

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