Research workbench
Cryo-EM structure of a single dynein tail domain bound to dynactin and BICD2N
Analyse Cryo-EM structure of a single dynein tail domain bound to dynactin and BICD2N in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F3A
- Type
- protein
- Length
- 9,810 residues
- Chains
- 36
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ARP1 actin related protein 1 homolog a; Actin, cytoplasmic 1; Actin related protein 10…
- UniProt
- F2Z5G5, Q6QAQ1, I3LHK5, A0PFK5, A9XFX6, D0G6S1, A0A286ZK88, F1SKF9, Q14204, Q13409, O43237, Q9NP97
- Ligands
- ADP, ATP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 25 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, I | ARP1 actin related protein 1 homolog a | protein | 370 | 40% helix, 14% strand | F2Z5G5 |
| H | Actin, cytoplasmic 1 | protein | 370 | 42% helix, 13% strand | Q6QAQ1 |
| J | Actin related protein 10 homolog | protein | 369 | 41% helix, 15% strand | I3LHK5 |
| K | Capping protein (actin filament) muscle Z-line, alpha 1 | protein | 278 | 39% helix, 26% strand | A0PFK5 |
| L | F-actin capping protein beta subunit | protein | 269 | 42% helix, 24% strand | A9XFX6 |
| M | Dynactin subunit 2 | protein | 587 | 94% helix, 0% strand | — |
| N | Dynactin subunit 2 | protein | 616 | 89% helix, 0% strand | — |
| O, P | Dynactin subunit 3 | protein | 65 | 42% helix, 25% strand | — |
| Q, R | Dynactin subunit 2 | protein | 87 | 90% helix, 0% strand | — |
| U | Dynactin 6 | protein | 171 | 13% helix, 14% strand | D0G6S1 |
| V | Dynactin subunit 5 | protein | 165 | 11% helix, 10% strand | A0A286ZK88 |
| Y | Dynactin subunit 4 | protein | 264 | 13% helix, 6% strand | — |
| Z | Dynactin subunit 1 | protein | 52 | 62% helix, 0% strand | — |
| a | Dynactin subunit 2 | protein | 52 | 27% helix, 8% strand | F1SKF9 |
| b | Dynactin subunit 2 | protein | 75 | 19% helix, 5% strand | F1SKF9 |
| c | Dynactin subunit 2 | protein | 35 | 11% helix, 6% strand | F1SKF9 |
| d | Dynactin subunit 2 | protein | 24 | 21% helix, 13% strand | F1SKF9 |
| e | Cytoplasmic dynein 1 heavy chain 1 | protein | 785 | 66% helix, 3% strand | Q14204 |
| f | Cytoplasmic dynein 1 heavy chain 1 | protein | 832 | 63% helix, 3% strand | Q14204 |
| g | Cytoplasmic dynein 1 intermediate chain 2 | protein | 397 | 9% helix, 32% strand | Q13409 |
| h | Cytoplasmic dynein 1 intermediate chain 2 | protein | 401 | 7% helix, 26% strand | Q13409 |
| j | Cytoplasmic dynein 1 light intermediate chain 2 | protein | 15 | 33% helix, 0% strand | O43237 |
| k, l | Dynein light chain roadblock-type 1 | protein | 93 | 34% helix, 26% strand | Q9NP97 |
| z | Dynactin subunit 1 | protein | 53 | 74% helix, 0% strand | — |
| 5, 6 | BICD2N | protein | 275 | 99% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 9 copies · chains A, B, C, D, E, F, G, I, J
- ATP · Adenosine-5'-triphosphate · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.86 | 0.87 | 176 | empty |
| 2 | 601 | 0.84 | 0.89 | 95 | empty |
| 3 | 1032 | 0.84 | 0.85 | 147 | empty |
| 4 | 1194 | 0.83 | 0.84 | 163 | ADP |
| 5 | 1062 | 0.82 | 0.84 | 152 | empty |
Interfaces
74 interfaces between chains.
- 5–6 · 2423 Ų buried · 0 hydrogen bonds · protein-protein
- e–f · 1466 Ų buried · 9 hydrogen bonds · protein-protein
- e–g · 1279 Ų buried · 6 hydrogen bonds · protein-protein
- K–L · 1183 Ų buried · 7 hydrogen bonds · protein-protein
- J–Y · 841 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- Q6QAQ1 · AlphaFold monomer V2.0 prediction for actin, cytoplasmic 1 (Q6QAQ1) · a predicted model of the same protein · chain H against A, TM-score 0.94
- Q13409 · AlphaFold monomer V2.0 prediction for cytoplasmic dynein 1 intermediate chain 2 (Q13409) · a predicted model of the same protein · chain g against A, TM-score 0.93
- Q9NP97 · AlphaFold monomer V2.0 prediction for dynein light chain roadblock- type 1 (Q9NP97) · a predicted model of the same protein · chain l against A, TM-score 0.91
- O43237 · AlphaFold monomer V2.0 prediction for cytoplasmic dynein 1 light intermediate chain 2… · a predicted model of the same protein · chain j against A, TM-score 0.41
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt F2Z5G5
- Every structure of UniProt Q6QAQ1
- Every structure of UniProt I3LHK5
- Every structure of UniProt A0PFK5
- Every structure of UniProt A9XFX6
- Every structure of UniProt D0G6S1
- Every structure of UniProt A0A286ZK88
- Every structure of UniProt F1SKF9
- Every structure of UniProt Q14204
- Every structure of UniProt Q13409
- Every structure of UniProt O43237
- Every structure of UniProt Q9NP97
- Elsewhere: RCSB PDB 6F3A · PDBe 6F3A · UniProt F2Z5G5 · UniProt Q6QAQ1 · UniProt I3LHK5 · UniProt A0PFK5 · UniProt A9XFX6 · UniProt D0G6S1 · UniProt A0A286ZK88 · UniProt F1SKF9 · UniProt Q14204 · UniProt Q13409 · UniProt O43237 · UniProt Q9NP97
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