6F3A: Single dynein tail domain
Cryo-EM structure of a single dynein tail domain bound to dynactin and BICD2N. Determined by electron microscopy at 8.2 Å resolution. Released 17 Jan 2018.
- Method
- Electron microscopy
- Resolution
- 8.2 Å
- Organisms
- Sus scrofa, Homo sapiens, Mus musculus
- Chains
- 36
- Atoms
- 48,864
- Mol. weight
- 1329.14 kDa
- Ligands
- ADP, ATP
- Released
- 17 Jan 2018
Explore 6F3A in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6F3A contains 373 α-helices and 374 β-strands across 36 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 | 2-274 | 273 | |
Chain a: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| β-strand | 21 | 1 | 64 |
| β-strand | 46-48 | 3 | 27 |
| α-helix | 52-60 | 9 | |
Chain A: 20 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-11 | 2 | |
| β-strand | 12-15 | 4 | 1 |
| β-strand | 22-24 | 3 | 1 |
| β-strand | 33-34 | 2 | 1 |
| β-strand | 39-42 | 4 | 2 |
| β-strand | 46 | 1 | 3 |
| α-helix | 60-64 | 5 | |
| α-helix | 66-68 | 3 | |
| β-strand | 69-72 | 4 | 2 |
| β-strand | 75-76 | 2 | 4 |
| β-strand | 79-80 | 2 | 4 |
| α-helix | 83-94 | 12 | |
| β-strand | 108-110 | 3 | 1 |
| α-helix | 118-126 | 9 | |
| α-helix | 127-131 | 5 | |
| β-strand | 137-139 | 3 | 1 |
| α-helix | 143-150 | 8 | |
| β-strand | 156-158 | 3 | 5 |
| β-strand | 165-169 | 5 | 5 |
| β-strand | 181-183 | 3 | 5 |
| α-helix | 187-200 | 14 | |
| α-helix | 208-220 | 13 | |
| α-helix | 228-232 | 5 | |
| β-strand | 240-242 | 3 | 6 |
| β-strand | 248-250 | 3 | 6 |
| α-helix | 254-257 | 4 | |
| α-helix | 258-262 | 5 | |
| α-helix | 265-267 | 3 | |
| α-helix | 275-283 | 9 | |
| α-helix | 288-296 | 9 | |
| β-strand | 298-300 | 3 | 5 |
| α-helix | 310-321 | 12 | |
| β-strand | 330 | 1 | 5 |
| α-helix | 336-349 | 14 | |
| α-helix | 353-356 | 4 | |
| β-strand | 358 | 1 | 1 |
| α-helix | 360-366 | 7 | |
| α-helix | 369-374 | 6 | |
Chain b: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| β-strand | 19-21 | 3 | 92 |
| β-strand | 47 | 1 | 82 |
| α-helix | 52-60 | 9 | |
Chain B: 21 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-16 | 5 | 11 |
| β-strand | 20-25 | 6 | 11 |
| β-strand | 33-36 | 4 | 11 |
| β-strand | 39-42 | 4 | 12 |
| β-strand | 46 | 1 | 13 |
| α-helix | 60-64 | 5 | |
| β-strand | 69-72 | 4 | 12 |
| α-helix | 83-94 | 12 | |
| β-strand | 108-112 | 5 | 11 |
| α-helix | 118-126 | 9 | |
| α-helix | 127-131 | 5 | |
| β-strand | 137-141 | 5 | 11 |
| α-helix | 143-150 | 8 | |
| β-strand | 155-158 | 4 | 14 |
| β-strand | 167-171 | 5 | 14 |
| β-strand | 174-175 | 2 | 14 |
| α-helix | 187-199 | 13 | |
| α-helix | 208-220 | 13 | |
| α-helix | 228-233 | 6 | |
| α-helix | 235-236 | 2 | |
| β-strand | 241-242 | 2 | 15 |
| α-helix | 243 | 1 | |
| β-strand | 248-249 | 2 | 15 |
| α-helix | 254-257 | 4 | |
| α-helix | 260-263 | 4 | |
| α-helix | 265-267 | 3 | |
| α-helix | 275-284 | 10 | |
| α-helix | 288-296 | 9 | |
| β-strand | 298-300 | 3 | 14 |
| α-helix | 310-321 | 12 | |
| β-strand | 330-331 | 2 | 14 |
| α-helix | 336-348 | 13 | |
| α-helix | 352-354 | 3 | |
| β-strand | 358 | 1 | 11 |
| α-helix | 359 | 1 | |
| α-helix | 360-365 | 6 | |
| α-helix | 368-375 | 8 | |
Chain c: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-8 | 4 | |
| β-strand | 12 | 1 | 48 |
| β-strand | 21 | 1 | 47 |
Chain C: 19 helices, 26 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-11 | 2 | |
| β-strand | 12-13 | 2 | 19 |
| β-strand | 15 | 1 | 20 |
| β-strand | 20-23 | 4 | 20 |
| β-strand | 25 | 1 | 19 |
| β-strand | 33-36 | 4 | 20 |
| β-strand | 39 | 1 | 21 |
| β-strand | 42 | 1 | 22 |
| β-strand | 45-46 | 2 | 23 |
| β-strand | 69 | 1 | 22 |
| β-strand | 72 | 1 | 21 |
| β-strand | 75 | 1 | 24 |
| β-strand | 80 | 1 | 24 |
| α-helix | 83-93 | 11 | |
| β-strand | 108-109 | 2 | 19 |
| β-strand | 110 | 1 | 25 |
| α-helix | 118-126 | 9 | |
| α-helix | 127-131 | 5 | |
| β-strand | 136-137 | 2 | 26 |
| β-strand | 139 | 1 | 25 |
| α-helix | 143-150 | 8 | |
| β-strand | 154-158 | 5 | 27 |
| β-strand | 167-171 | 5 | 27 |
| β-strand | 174 | 1 | 3 |
| α-helix | 187-200 | 14 | |
| α-helix | 208-220 | 13 | |
| β-strand | 223 | 1 | 28 |
| α-helix | 229-232 | 4 | |
| β-strand | 241-242 | 2 | 29 |
| α-helix | 243 | 1 | |
| β-strand | 248-249 | 2 | 29 |
| α-helix | 254-260 | 7 | |
| α-helix | 265-267 | 3 | |
| α-helix | 275-285 | 11 | |
| α-helix | 288-296 | 9 | |
| β-strand | 298-300 | 3 | 27 |
| α-helix | 303-305 | 3 | |
| β-strand | 308 | 1 | 28 |
| α-helix | 310-321 | 12 | |
| β-strand | 330-333 | 4 | 27 |
| α-helix | 336-349 | 14 | |
| α-helix | 353-356 | 4 | |
| β-strand | 358-359 | 2 | 26 |
| α-helix | 360-365 | 6 | |
| α-helix | 368-375 | 8 | |
Chain d: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-8 | 5 | |
| β-strand | 19-21 | 3 | 72 |
27 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 |
| Dynactin Subunit 4 | Y | protein | 264 | Sus scrofa | |
9 more molecules are not listed.
Sequence of entity 1 (A, B, C, D, E, F, G, I), FASTA
>6F3A_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
>6F3A_2 Actin, cytoplasmic 1 (chains H)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF
Sequence of entity 3 (J), FASTA
>6F3A_3 Actin related protein 10 homolog (chains J)
MPLYEGLGSGGEKTAVVIDLGEAFTKCGFAGETGPRCIIPSVIKKAGMPKPIKVVQYNIN
TEELYSYLKEFIHILYFRHLLVNPRDRRVVVIESVLCPSHFRETLTRVLFKYFEVPSVLL
APSHLMALLTLGINSAMVLDCGYRESLVLPIYEGIPVLNCWGALPLGGKALHKELETQLL
EQCTVDTGAAKEQSLPSVMGSIPEGVLEDIKVRTCFVSDLTRGLKIQAAKFNIDGNTERP
SPPPNVDYPLDGEKILHVLGSIRDSVVEILFEQDNEEKSVATLILDSLMQCPIDTRKQLA
ENLVIIGGTSMLPGFLHRLLAEIRYLVEKPKYKKTLGTKTFRIHTPPAKANCVAWLGGAI
FGALQDILGSRSVSKEYYNQTGRIPDWCSL
Sequence of entity 4 (K), FASTA
>6F3A_4 Capping protein (Actin filament) muscle Z-line, alpha 1 (chains K)
MADFEDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMD
QFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVDGSLKSW
RESCDSALRAYVKDHYSNGFCTVYAKNIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFT
ITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSVTVSNEAQTAKEFIKIIEHAENEYQ
TAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQNA
Sequence of entity 5 (L), FASTA
>6F3A_5 F-actin capping protein beta subunit (chains L)
MSDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYL
LCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVY
LWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTN
KSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIV
NGLRSVQTFADKSKQEALKNDLVEALKRKQQC
Sequence of entity 6 (M), FASTA
>6F3A_6 Dynactin Subunit 2 (chains M)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Sequence of entity 7 (N), FASTA
>6F3A_7 Dynactin Subunit 2 (chains N)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXX
Sequence of entity 8 (O, P), FASTA
>6F3A_8 Dynactin Subunit 3 (chains O, P)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXX
Sequence of entity 9 (Q, R), FASTA
>6F3A_9 Dynactin Subunit 2 (chains Q, R)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXX
Sequence of entity 10 (U), FASTA
>6F3A_10 Dynactin 6 (chains U)
MAEKTQKSVKIAPGAVVCVESEIRGDVTIGPRTVIHPKARIIAEAGPIVIGEGNLIEEQA
LIINAHPDNITPDAEDSEPKPMIIGTNNVFEVGCYSQAMKMGDNNVIESKAYVGRNVILT
SGCIIGACCNLNTFEVIPENTVIYGADCLRRVQTERPQPQTLQLDFLMKILPNYHHLKKT
MKGSSTPVKN
Sequence of entity 11 (V), FASTA
>6F3A_11 Dynactin subunit 5 (chains V)
MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTIVMNDCIIRGDLANVRVGRH
CVVKSRSVIRPPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRC
VLKDCCKILDNTVLPPETVVPPFTVFSGCPGLFSGELPECTQELMIDVTKSYYQKFLPLT
QV
Sequence of entity 12 (Y), FASTA
>6F3A_12 Dynactin Subunit 4 (chains Y)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXX
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
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
- 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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