› 5afu

Electron Microscopy
3.5Å resolution

Cryo-EM structure of dynein tail-dynactin-BICD2N complex

Released:
DOI: 10.2210/pdb5afu/pdb
PDB entry 5afu coloured by chain, front view.
PDB entry 5afu coloured by chain, side view.
PDB entry 5afu coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
The structure of the dynactin complex and its interaction with dynein.
Urnavicius L, Zhang K, Diamant AG, Motz C, Schlager MA, Yu M, Patel NA, Robinson CV, Carter AP
Science 347 1441-1446 (2015)
PMID: 25814576
Related structures: EMD-2860

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 33-mer (preferred)
PDBe Complex ID:
PDB-CPX-102283 (preferred)
Entry contents:
22 distinct polypeptide molecules
Macromolecules (22 distinct):
DYNEIN TAIL Chain: 1
Molecule details ›
Chain: 1
Length: 361 amino acids
Theoretical weight: 30.74 KDa
Source organism: Sus scrofa
DYNEIN TAIL Chain: 2
Molecule details ›
Chain: 2
Length: 359 amino acids
Theoretical weight: 30.57 KDa
Source organism: Sus scrofa
Dynein tail Chains: 3, 4
Molecule details ›
Chains: 3, 4
Length: 350 amino acids
Theoretical weight: 38.9 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0J9X2A1 (Residues: 1-350; Coverage: 100%)
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
DYNEIN TAIL Chains: 5, 6
Molecule details ›
Chains: 5, 6
Length: 275 amino acids
Theoretical weight: 23.42 KDa
Source organism: Sus scrofa
Alpha-centractin Chains: A, B, C, D, E, F, G, I
Molecule details ›
Chains: A, B, C, D, E, F, G, I
Length: 370 amino acids
Theoretical weight: 41.96 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F2Z5G5 (Residues: 7-310; Coverage: 87%)
Gene name: ACTR1A
Sequence domains: Actin
Structure domains:
Actin, cytoplasmic 1 Chain: H
Molecule details ›
Chain: H
Length: 370 amino acids
Theoretical weight: 41.19 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q6QAQ1 (Residues: 6-375; Coverage: 99%)
Gene name: ACTB
Sequence domains: Actin
Structure domains:
Actin-related protein 10 Chain: J
Molecule details ›
Chain: J
Length: 379 amino acids
Theoretical weight: 42.14 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LHK5 (Residues: 12-390; Coverage: 91%)
Gene names: ACTR10, ARP11
Sequence domains: Actin
F-actin-capping protein subunit alpha-1 Chain: K
Molecule details ›
Chain: K
Length: 275 amino acids
Theoretical weight: 31.78 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0PFK5 (Residues: 7-281; Coverage: 96%)
Gene names: CAPZA1, CP alpha1, Capza
Sequence domains: F-actin capping protein alpha subunit
Structure domains:
F-actin-capping protein subunit beta Chain: L
Molecule details ›
Chain: L
Length: 270 amino acids
Theoretical weight: 30.51 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: D2JYW4 (Residues: 2-271; Coverage: 98%)
Gene name: CAPZB
Sequence domains: F-actin capping protein, beta subunit
Structure domains:
DYNACTIN Chain: M
Molecule details ›
Chain: M
Length: 587 amino acids
Theoretical weight: 49.97 KDa
Source organism: Sus scrofa
DYNACTIN 6 Chain: N
Molecule details ›
Chain: N
Length: 616 amino acids
Theoretical weight: 52.44 KDa
Source organism: Sus scrofa
DYNACTIN Chains: O, P
Molecule details ›
Chains: O, P
Length: 65 amino acids
Theoretical weight: 5.55 KDa
Source organism: Sus scrofa
DYNACTIN Chains: Q, R
Molecule details ›
Chains: Q, R
Length: 87 amino acids
Theoretical weight: 7.42 KDa
Source organism: Sus scrofa
Dynactin subunit 6 Chain: U
Molecule details ›
Chain: U
Length: 168 amino acids
Theoretical weight: 18.34 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: D0G6S1 (Residues: 13-185; Coverage: 88%)
Gene name: DCTN6
Structure domains: Hexapeptide repeat proteins
Dynactin subunit 5 Chain: V
Molecule details ›
Chain: V
Length: 165 amino acids
Theoretical weight: 18.18 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZK88 (Residues: 18-182; Coverage: 91%)
Gene name: DCTN5
Sequence domains: Dynactin subunit 5
Structure domains: Hexapeptide repeat proteins
F-ACTIN-CAPPING PROTEIN SUBUNIT BETA Chain: Y
Molecule details ›
Chain: Y
Length: 243 amino acids
Theoretical weight: 20.7 KDa
Source organism: Sus scrofa
F-ACTIN-CAPPING PROTEIN SUBUNIT BETA Chain: Z
Molecule details ›
Chain: Z
Length: 52 amino acids
Theoretical weight: 4.44 KDa
Source organism: Sus scrofa
Dynactin subunit 2 Chain: a
Molecule details ›
Chain: a
Length: 48 amino acids
Theoretical weight: 5.4 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0J9X292 (Residues: 1-48; Coverage: 100%)
Dynactin subunit 2 Chain: b
Molecule details ›
Chain: b
Length: 71 amino acids
Theoretical weight: 7.93 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0J9X293 (Residues: 1-71; Coverage: 100%)
Sequence domains: Dynamitin
Dynactin Chain: c
Molecule details ›
Chain: c
Length: 31 amino acids
Theoretical weight: 3.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0J9X299 (Residues: 1-31; Coverage: 100%)
Dynactin Chain: d
Molecule details ›
Chain: d
Length: 20 amino acids
Theoretical weight: 2.24 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0J9X295 (Residues: 1-20; Coverage: 100%)
F-ACTIN-CAPPING PROTEIN SUBUNIT BETA Chain: z
Molecule details ›
Chain: z
Length: 53 amino acids
Theoretical weight: 4.53 KDa
Source organism: Sus scrofa

Ligands and Environments

2 bound ligands:
Ligand ADP 9 x ADP
Ligand ATP 1 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-2860

Quick links

Citations

52 review citations

The cytoplasmic dynein transport machinery and its many cargoes.
Reck-Peterson et al. (2018)
51 more

6 mentions without citation

Structure and Mechanics of Dynein Motors.
Canty et al. (2021)
5 more