8PR4: Dynactin pointed end

Dynactin pointed end bound to JIP3. Determined by electron microscopy at 3.5 Å resolution. Released 27 Mar 2024.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 6
Atoms: 9,494
Mol. weight: 272.68 kDa
Ligands: ZN, ATP
Released: 27 Mar 2024

Explore 8PR4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PR4 contains 49 α-helices and 101 β-strands across 6 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 J: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
β-strand	16-19	4	1
β-strand	24-29	6	1
β-strand	37-40	4	1
β-strand	42-43	2	2
α-helix	51	1
β-strand	52-53	2	2
α-helix	61-78	18
β-strand	89-93	5	1
α-helix	99-107	9
α-helix	108-112	5
β-strand	117-122	6	1
α-helix	125-128	4
β-strand	135-141	7	3
β-strand	146-152	7	3
β-strand	155-156	2	3
α-helix	158-160	3
β-strand	162-164	3	3
α-helix	168-181	14
β-strand	185-186	2	4
β-strand	195	1	4
α-helix	204-213	10
α-helix	220-231	12
α-helix	241-245	5
β-strand	246-250	5	4
β-strand	254-258	5	4
α-helix	262-265	4
α-helix	267-269	3
α-helix	282-288	7
α-helix	297-300	4
β-strand	303	1	3
β-strand	306	1	3
α-helix	315-326	12
α-helix	330-336	7
β-strand	343	1	3
α-helix	353-362	10
α-helix	365-368	4
β-strand	373-374	2	1
α-helix	375-380	6

Chain U: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	5
α-helix	12	1
β-strand	16-17	2	6
β-strand	18	1	7
β-strand	23-24	2	8
β-strand	27-29	3	5
β-strand	34-35	2	6
β-strand	41-42	2	8
β-strand	48-50	3	5
β-strand	55-56	2	6
β-strand	61-63	3	8
α-helix	66-69	4
β-strand	82-84	3	5
β-strand	90	1	6
β-strand	95-96	2	8
β-strand	100-101	2	5
β-strand	106-107	2	6
β-strand	112-113	2	8
β-strand	117-119	3	5
β-strand	124-125	2	6
β-strand	130-131	2	8
β-strand	135-137	3	5
β-strand	141	1	9
β-strand	142-143	2	6
β-strand	153	1	9
α-helix	157-159	3
α-helix	162-167	6
β-strand	177	1	7

Chain W: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	10
β-strand	13-15	3	11
β-strand	21-23	3	11
β-strand	28-29	2	12
β-strand	35-36	2	13
β-strand	41-42	2	11
β-strand	48-49	2	12
β-strand	56-57	2	13
β-strand	62-63	2	11
β-strand	68-69	2	12
β-strand	73-74	2	14
β-strand	81-82	2	14
β-strand	86	1	13
β-strand	92-93	2	11
β-strand	98-99	2	12
β-strand	104	1	15
β-strand	109-110	2	11
β-strand	115-116	2	12
β-strand	121-122	2	15
β-strand	127-128	2	11
β-strand	133-134	2	12
α-helix	135	1
β-strand	139-140	2	15
α-helix	141	1
β-strand	144-147	4	11
β-strand	152-156	5	11
α-helix	165-174	10
β-strand	176-178	3	10

Chain x: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	411-466	56
α-helix	519-539	21
α-helix	541-550	10

Chain X: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	383-386	4
α-helix	392-395	4
α-helix	413-466	54
α-helix	519-548	30

Chain Y: 15 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	16
β-strand	21-22	2	16
α-helix	24-26	3
β-strand	27-30	4	17
β-strand	35-38	4	17
β-strand	43-44	2	18
β-strand	48-50	3	19
β-strand	57-58	2	19
α-helix	60-65	6
β-strand	69-75	7	20
β-strand	82	1	20
β-strand	84-87	4	21
β-strand	107-110	4	21
β-strand	117	1	21
α-helix	123-125	3
β-strand	126	1	21
α-helix	135-138	4
α-helix	139-141	3
α-helix	142-169	28
α-helix	226-228	3
β-strand	229	1	3
β-strand	249	1	22
α-helix	250-251	2
α-helix	252-255	4
β-strand	265	1	22
α-helix	266-268	3
α-helix	270-271	2
β-strand	272-275	4	20
α-helix	276	1
β-strand	277-279	3	19
β-strand	282-283	2	18
β-strand	290-294	5	18
α-helix	295	1
β-strand	303-306	4	18
β-strand	308	1	17
α-helix	309-311	3
β-strand	316-320	5	23
β-strand	328-335	8	23
β-strand	340-344	5	16
β-strand	363	1	23
β-strand	370-373	4	16
β-strand	399-403	5	23
β-strand	406-413	8	23
β-strand	423-430	8	16
β-strand	432	1	24
α-helix	449-451	3
β-strand	452	1	24
β-strand	455-461	7	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Arp11	J	protein	417	Sus scrofa	I3LHK5 (AlphaFold model)
Dynactin 6	U	protein	190	Sus scrofa	D0G6S1 (AlphaFold model)
Dynactin subunit 5	W	protein	182	Sus scrofa	A0A286ZK88 (AlphaFold model)
Dynactin subunit 4	Y	protein	467	Sus scrofa	A0A4X1TB62 (AlphaFold model)
C-Jun-amino-terminal kinase-interacting protein 3	X, x	protein	581	Homo sapiens	Q9UPT6

Sequence of entity 1 (J), FASTA

>8PR4_1 Arp11 (chains J)
MPLYEGLGSGGEKTAVVIDLGEAFTKCGFAGETGPRCIIPSVIKKAGMPKPIKVVQYNIN
TEELYSYLKEFIHILYFRHLLVNPRDRRVVVIESVLCPSHFRETLTRVLFKYFEVPSVLL
APSHLMALLTLGINSAMVLDCGYRESLVLPIYEGIPVLNCWGALPLGGKALHKELETQLL
EQCTVDTGAAKEQSLPSVMGSIPEGVLEDIKVRTCFVSDLTRGLKIQAAKFNIDGNTERP
SPPPNVDYPLDGEKILHVLGSIRDSVVEILFEQDNEEKSVATLILDSLMQCPIDTRKQLA
ENLVIIGGTSMLPGFLHRLLAEIRYLVEKPKYKKTLGTKTFRIHTPPAKANCVAWLGGAI
FGALQDILGSRSVSKEYYNQTGRIPDWCSLNNPPLEMVFDVGKSQPPLMKRAFSTEK

Sequence of entity 2 (U), FASTA

>8PR4_2 Dynactin 6 (chains U)
MAEKTQKSVKIAPGAVVCVESEIRGDVTIGPRTVIHPKARIIAEAGPIVIGEGNLIEEQA
LIINAHPDNITPDAEDSEPKPMIIGTNNVFEVGCYSQAMKMGDNNVIESKAYVGRNVILT
SGCIIGACCNLNTFEVIPENTVIYGADCLRRVQTERPQPQTLQLDFLMKILPNYHHLKKT
MKGSSTPVKN

Sequence of entity 3 (W), FASTA

>8PR4_3 Dynactin subunit 5 (chains W)
MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTIVMNDCIIRGDLANVRVGRH
CVVKSRSVIRPPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRC
VLKDCCKILDNTVLPPETVVPPFTVFSGCPGLFSGELPECTQELMIDVTKSYYQKFLPLT
QV

Sequence of entity 4 (Y), FASTA

>8PR4_4 Dynactin subunit 4 (chains Y)
MASLLQSERVLYLVQGEKKVRAPLSQLYFCRYCSELRSLECVSHEVDSHYCPSCLENMPS
AEAKLKKNRCANCFDCPGCMHTLSTRATSISTQLPDDPAKTAVKKAYYLACGFCRWTSRD
VGMADKSVASGGWQEPDHPHTQRMNKLIEYYQQLAQKEKVERDRKKLARRRNYMPLAFSQ
HTIHVVDKYGLGTRLQRPRAGTTITALAGLSLKEGEDQKEIKIEPAQAVDEVEPLPEDYY
TRPVNLTEVTTLQQRLLQPDFQPICASQLYPRHKHLLIKRSLRCRQCEHNLSKPEFNPTS
IKFKIQLVAVNYIPEVRIMSIPNLRYMKESQVLLTLTNPVENLTHVTLLECEEGDPDDTN
STAKVSVPPTELVLAGKDAAAEYDELAEPQDFPDDPDVVAFRKANKVGVFIKVTPQREEG
DVTVCFKLKHDFKNLAAPIRPVEEADPGAEVSWLTQHVELSLGPLLP

Sequence of entity 5 (X, x), FASTA

>8PR4_5 C-Jun-amino-terminal kinase-interacting protein 3 (chains X, x)
SNIEFLKMMEIQMDEGGGVVVYQDDYCSGSVMSERVSGLAGSIYREFERLIHCYDEEVVK
ELMPLVVNVLENLDSVLSENQEHEVELELLREDNEQLLTQYEREKALRRQAEEKFIEFED
ALEQEKKELQIQVEHYEFQTRQLELKAKNYADQISRLEERESEMKKEYNALHQRHTEMIQ
TYVEHIERSKMQQVGGNSQTESSLPGRRKERPTSLNVFPLADGTVRAQIGGKLVPAGDHW
HLSDLGQLQSSSSYQCPQDEMSESGQSSAAATPSTTGTKSNTPTSSVPSAAVTPLNESLQ
PLGDYGVGSKNSKRAREKRDSRNMEVQVTQEMRNVSIGMGSSDEWSDVQDIIDSTPELDM
CPETRLDRTGSSPTQGIVNKAFGINTDSLYHELSTAGSEVIGDVDEGADLLGEFSVRDDF
FGMGKEVGNLLLENSQLLETKNALNVVKNDLIAKVDQLSGEQEVLRGELEAAKQAKVKLE
NRIKELEEELKRVKSEAIIARREPKEEAEDVSSYLCTESDKIPMAQRRRFTRVEMARVLM
ERNQYKERLMELQEAVRWTEMIRASREGSGSGRWSHPQFEK

Ligands and cofactors

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

Primary citation

Molecular mechanism of dynein-dynactin complex assembly by LIS1. Singh, K., Lau, C.K., Manigrasso, G. et al. Science (2024) 383:eadk8544-eadk8544. DOI 10.1126/science.adk8544 · PubMed

Other PDB entries of the same protein (UniProt I3LHK5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z8M 3.37 Å, The pointed end complex of dynactin bound to BICDR1
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
9DGS 3.9 Å, Dynactin and dynein tail region of dynein-dynactin complex on microtubules
5ADX 4.0 Å, CryoEM structure of dynactin complex at 4.0 angstrom resolution
9YNG 4.07 Å, Dynactin and dynein-1 tail region of dynein-dynactin complex on microtubule in the…
6ZNM 4.1 Å, The pointed end complex of dynactin 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
9DGU 7.1 Å, structure of dynactin, dynein tail with two BICDR from dynein-dynactin-BICDR on…

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