5NW4: Human cytoplasmic dynein-1

Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2. Determined by electron microscopy at 8.7 Å resolution. Released 2 Aug 2017.

Method: Electron microscopy
Resolution: 8.7 Å
Organisms: Homo sapiens, Sus scrofa
Chains: 39
Atoms: 66,297
Mol. weight: 1095.06 kDa
Released: 2 Aug 2017

Explore 5NW4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NW4 contains 431 α-helices and 417 β-strands across 39 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: 6 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	26
β-strand	75-77	3	26
α-helix	84-89	6
β-strand	118	1	27
α-helix	126-144	19
α-helix	158-178	21

Chain 2: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	8-21	14
α-helix	32-50	19
β-strand	63-65	3	32
β-strand	77	1	32
α-helix	83-89	7
β-strand	96-98	3	32
β-strand	116	1	27
β-strand	117-118	2	32
α-helix	126-144	19
α-helix	158-178	21

Chain 5: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	181-453	273

Chain 6: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	456-728	273

Chain a: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	2-43	42
α-helix	46-71	26
α-helix	76-165	90
α-helix	202-237	36
α-helix	243-262	20
α-helix	267-361	95
α-helix	402-437	36
α-helix	444-459	16
α-helix	466-552	87
α-helix	602-624	23
α-helix	702-740	39
α-helix	802-823	22

Chain A: 36 helices, 0 β-strands

Element	Residues	Length
α-helix	190-197	8
α-helix	217-236	20
α-helix	249-269	21
α-helix	275-283	9
α-helix	291-311	21
α-helix	329-344	16
α-helix	352-373	22
α-helix	382-416	35
α-helix	427-452	26
α-helix	459-473	15
α-helix	485-512	28
α-helix	520-526	7
α-helix	535-568	34
α-helix	577-603	27
α-helix	616-643	28
α-helix	680-717	38
α-helix	729-741	13
α-helix	754-766	13
α-helix	774-786	13
α-helix	805-816	12
α-helix	819-852	34
α-helix	863-886	24
α-helix	916-949	34
α-helix	969-993	25
α-helix	999-1009	11
α-helix	1013-1024	12
α-helix	1034-1069	36
α-helix	1104-1115	12
α-helix	1118-1159	42
α-helix	1191-1209	19
α-helix	1210-1214	5
α-helix	1215-1222	8
α-helix	1255-1284	30
α-helix	1317-1353	37
α-helix	1357-1388	32
α-helix	1392-1420	29

Chain b: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	2-38	37
α-helix	45-73	29
α-helix	78-166	89
α-helix	202-239	38
α-helix	242-268	27
α-helix	277-362	86
α-helix	402-433	32
α-helix	434-436	3
α-helix	440-463	24
α-helix	467-552	86
α-helix	603-625	23
α-helix	702-744	43
α-helix	761-767	7
α-helix	802-817	16

Chain B: 35 helices, 0 β-strands

Element	Residues	Length
α-helix	190-197	8
α-helix	217-236	20
α-helix	249-269	21
α-helix	275-283	9
α-helix	291-311	21
α-helix	329-344	16
α-helix	352-373	22
α-helix	382-416	35
α-helix	427-453	27
α-helix	459-473	15
α-helix	486-513	28
α-helix	520-526	7
α-helix	535-568	34
α-helix	577-603	27
α-helix	615-642	28
α-helix	691-717	27
α-helix	729-741	13
α-helix	754-766	13
α-helix	774-786	13
α-helix	807-816	10
α-helix	819-852	34
α-helix	863-886	24
α-helix	916-949	34
α-helix	969-993	25
α-helix	999-1008	10
α-helix	1040-1069	30
α-helix	1104-1115	12
α-helix	1118-1159	42
α-helix	1191-1209	19
α-helix	1210-1214	5
α-helix	1215-1222	8
α-helix	1255-1284	30
α-helix	1317-1353	37
α-helix	1357-1387	31
α-helix	1391-1420	30

30 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 heavy chain	B	protein	889	Homo sapiens
dynein intermediate chain	D	protein	341	Homo sapiens
dynein intermediate chain	C	protein	350	Homo sapiens
dynein heavy chain	A	protein	922	Homo sapiens
dynein N-terminal dimerization domain	1	protein	125	Homo sapiens
dynein N-terminal dimerization domain	2	protein	124	Homo sapiens
Robl	R, S	protein	120	Homo sapiens
dynein light intermediate chain	E	protein	295	Homo sapiens
dynein light intermediate chain	F	protein	298	Homo sapiens
Arp1	G, H, O, P, Q, T, U, W	protein	376	Sus scrofa	F2Z5G5 (AlphaFold model)
beta-actin	V	protein	396	Sus scrofa	A0A151MAL5 (AlphaFold model)
Arp11	X	protein	417	Sus scrofa	I3LHK5 (AlphaFold model)

16 more molecules are not listed.

Sequence of entity 1 (B), FASTA

>5NW4_1 dynein heavy chain (chains B)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 2 (D), FASTA

>5NW4_2 dynein intermediate chain (chains D)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 3 (C), FASTA

>5NW4_3 dynein intermediate chain (chains C)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 4 (A), FASTA

>5NW4_4 dynein heavy chain (chains A)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 5 (1), FASTA

>5NW4_5 dynein N-terminal dimerization domain (chains 1)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXX

Sequence of entity 6 (2), FASTA

>5NW4_6 dynein N-terminal dimerization domain (chains 2)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXX

Sequence of entity 7 (R, S), FASTA

>5NW4_7 Robl (chains R, S)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 8 (E), FASTA

>5NW4_8 dynein light intermediate chain (chains E)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 9 (F), FASTA

>5NW4_9 dynein light intermediate chain (chains F)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 10 (G, H, O, P, Q, T, U, W), FASTA

>5NW4_10 Arp1 (chains G, H, O, P, Q, T, U, W)
MESYDVIANQPVVIDNGSGVIKAGFAGDQIPKYCFPNYVGRPKHVRVMAGALEGDIFIGP
KAEEHRGLLSIRYPMEHGIVKDWNDMERIWQYVYSKEQLQTFSEEHPVLLTEAPLNPRKN
RERAAEVFFETFNVPALFISMQAVLSLYATGRTTGVVLDSGDGVTHAVPIYEGFAMPHSI
MRIDIAGRDVSRFLRLYLRKEGYDFHSSSEFEIVKAIKERACYLSINPQKDETLETEKAQ
YYLPDGSTIEIGPSRFRAPELLFRPDLIGEESEGIHEVLVFAIQKSDMDLRRTLFSNIVL
SGGSTLFKGFGDRLLSEVKKLAPKDVKIRISAPQERLYSTWIGGSILASLDTFKKMWVSK
KEYEEDGARSIHRKTF

Sequence of entity 11 (V), FASTA

>5NW4_11 beta-actin (chains V)
MSVRSARRASASAEAELLQTMGDEEIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPR
HQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPE
EHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGV
THTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYV
ALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTF
NSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSV
WIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF

Sequence of entity 12 (X), FASTA

>5NW4_12 Arp11 (chains X)
MPLYEGLGSGGEKTAVVIDLGEAFTKCGFAGETGPRCIIPSVIKKAGMPKPIKVVQYNIN
TEELYSYLKEFIHILYFRHLLVNPRDRRVVVIESVLCPSHFRETLTRVLFKYFEVPSVLL
APSHLMALLTLGINSAMVLDCGYRESLVLPIYEGIPVLNCWGALPLGGKALHKELETQLL
EQCTVDTGAAKEQSLPSVMGSIPEGVLEDIKVRTCFVSDLTRGLKIQAAKFNIDGNTERP
SPPPNVDYPLDGEKILHVLGSIRDSVVEILFEQDNEEKSVATLILDSLMQCPIDTRKQLA
ENLVIIGGTSMLPGFLHRLLAEIRYLVEKPKYKKTLGTKTFRIHTPPAKANCVAWLGGAI
FGALQDILGSRSVSKEYYNQTGRIPDWCSLNNPPLEMVFDVGKSQPPLMKRAFSTEK

Primary citation

Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated. Zhang, K., Foster, H.E., Rondelet, A. et al. Cell (2017) 169:1303-1314.e18. DOI 10.1016/j.cell.2017.05.025 · 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

Browse structure collections

About this viewer

MolViewer shows 5NW4 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.