5NW4 image
Deposition Date 2017-05-05
Release Date 2017-08-02
Last Version Date 2024-11-13
Entry Detail
PDB ID:
5NW4
Keywords:
Title:
Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Sus scrofa (Taxon ID: 9823)
Host Organism:
Method Details:
Experimental Method:
Resolution:
8.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:dynein N-terminal dimerization domain
Chain IDs:E (auth: 1)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:dynein N-terminal dimerization domain
Chain IDs:F (auth: 2)
Chain Length:124
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:BICD2N
Chain IDs:LA (auth: 5), MA (auth: 6)
Chain Length:275
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:dynein heavy chain
Chain IDs:D (auth: A)
Chain Length:922
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:dynein heavy chain
Chain IDs:A (auth: B)
Chain Length:889
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:dynein intermediate chain
Chain IDs:C
Chain Length:350
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:dynein intermediate chain
Chain IDs:B (auth: D)
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:dynein light intermediate chain
Chain IDs:I (auth: E)
Chain Length:174
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:dynein light intermediate chain
Chain IDs:J (auth: F)
Chain Length:174
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Arp1
Gene (Uniprot):ACTR1A
Chain IDs:K (auth: G), L (auth: H), M (auth: O), N (auth: P), O (auth: Q), P (auth: T), Q (auth: U), S (auth: W)
Chain Length:376
Number of Molecules:8
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:Robl
Chain IDs:G (auth: R), H (auth: S)
Chain Length:120
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:beta-actin
Chain IDs:R (auth: V)
Chain Length:396
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Arp11
Gene (Uniprot):ACTR10
Chain IDs:T (auth: X)
Chain Length:417
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Capping protein (Actin filament) muscle Z-line, alpha 1
Gene (Uniprot):CAPZA1
Chain IDs:U (auth: Y)
Chain Length:286
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:F-actin capping protein beta subunit variant II
Gene (Uniprot):CAPZB
Chain IDs:V (auth: Z)
Chain Length:293
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:dynactin shoulder complex
Chain IDs:W (auth: a)
Chain Length:922
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:dynactin shoulder complex
Chain IDs:X (auth: b)
Chain Length:889
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:dynactin shoulder complex
Chain IDs:Y (auth: c), Z (auth: d)
Chain Length:350
Number of Molecules:2
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:dynactin shoulder complex
Chain IDs:AA (auth: e), BA (auth: f)
Chain Length:174
Number of Molecules:2
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Dynactin 6
Gene (Uniprot):DCTN6
Chain IDs:CA (auth: g)
Chain Length:376
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Dynactin subunit 5
Chain IDs:DA (auth: h)
Chain Length:376
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:dynactin pointed end p62
Chain IDs:EA (auth: i)
Chain Length:243
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:p150
Chain IDs:FA (auth: j)
Chain Length:52
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Dynactin
Chain IDs:GA (auth: k)
Chain Length:48
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Dynactin
Chain IDs:HA (auth: l)
Chain Length:71
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Dynactin
Chain IDs:IA (auth: m)
Chain Length:31
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Dynactin
Chain IDs:JA (auth: n)
Chain Length:20
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:dynactin p150
Chain IDs:KA (auth: o)
Chain Length:376
Number of Molecules:1
Biological Source:Sus scrofa
Ligand Molecules
Primary Citation
Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated.
Cell 169 1303 1314.e18 (2017)
PMID: 28602352 DOI: 10.1016/j.cell.2017.05.025

Abstact

Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves poorly on its own or how it is activated by dynactin. Here, we present a cryoelectron microscopy structure of the complete 1.4-megadalton human dynein-1 complex in an inhibited state known as the phi-particle. We reveal the 3D structure of the cargo binding dynein tail and show how self-dimerization of the motor domains locks them in a conformation with low microtubule affinity. Disrupting motor dimerization with structure-based mutagenesis drives dynein-1 into an open form with higher affinity for both microtubules and dynactin. We find the open form is also inhibited for movement and that dynactin relieves this by reorienting the motor domains to interact correctly with microtubules. Our model explains how dynactin binding to the dynein-1 tail directly stimulates its motor activity.

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Primary Citation of related structures