› 6f38

Electron Microscopy
6.7Å resolution

Cryo-EM structure of two dynein tail domains bound to dynactin and HOOK3

Released:
DOI: 10.2210/pdb6f38/pdb
PDB entry 6f38 coloured by chain, front view.
PDB entry 6f38 coloured by chain, side view.
PDB entry 6f38 coloured by chain, top view.
Source organisms:
Primary publication:
Cryo-EM shows how dynactin recruits two dyneins for faster movement.
Urnavicius L, Lau CK, Elshenawy MM, Morales-Rios E, Motz C, Yildiz A, Carter AP
Nature 554 202-206 (2018)
PMID: 29420470
Related structures: EMD-4177

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 45-mer (preferred)
PDBe Complex ID:
PDB-CPX-104027 (preferred)
Entry contents:
23 distinct polypeptide molecules
Macromolecules (23 distinct):
Alpha-centractin Chains: A, B, C, D, E, F, G, I
Molecule details ›
Chains: A, B, C, D, E, F, G, I
Length: 376 amino acids
Theoretical weight: 42.67 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F2Z5G5 (Residues: 1-310; Coverage: 89%)
Gene name: ACTR1A
Sequence domains: Actin
Actin, cytoplasmic 1 Chain: H
Molecule details ›
Chain: H
Length: 375 amino acids
Theoretical weight: 41.78 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q6QAQ1 (Residues: 1-375; Coverage: 100%)
Gene name: ACTB
Sequence domains: Actin
Actin-related protein 10 Chain: J
Molecule details ›
Chain: J
Length: 390 amino acids
Theoretical weight: 43.2 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LHK5 (Residues: 1-390; Coverage: 94%)
Gene names: ACTR10, ARP11
Sequence domains: Actin
F-actin-capping protein subunit alpha-1 Chain: K
Molecule details ›
Chain: K
Length: 286 amino acids
Theoretical weight: 33.06 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0PFK5 (Residues: 1-286; Coverage: 100%)
Gene names: CAPZA1, CP alpha1, Capza
Sequence domains: F-actin capping protein alpha subunit
F-actin-capping protein subunit beta Chain: L
Molecule details ›
Chain: L
Length: 272 amino acids
Theoretical weight: 30.67 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0PFK7 (Residues: 1-272; Coverage: 100%)
Gene name: CAPZB
Sequence domains: F-actin capping protein, beta subunit
Dynactin Subunit 2 Chain: M
Molecule details ›
Chain: M
Length: 587 amino acids
Theoretical weight: 49.97 KDa
Source organism: Sus scrofa
Dynactin Subunit 2 Chain: N
Molecule details ›
Chain: N
Length: 616 amino acids
Theoretical weight: 52.44 KDa
Source organism: Sus scrofa
Dynactin Subunit 3 Chains: O, P
Molecule details ›
Chains: O, P
Length: 65 amino acids
Theoretical weight: 5.55 KDa
Source organism: Sus scrofa
Dynactin Subunit 2 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: 190 amino acids
Theoretical weight: 20.7 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: D0G6S1 (Residues: 1-190; Coverage: 100%)
Gene name: DCTN6
Dynactin subunit 5 Chain: V
Molecule details ›
Chain: V
Length: 182 amino acids
Theoretical weight: 20.15 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZK88 (Residues: 1-182; Coverage: 100%)
Gene name: DCTN5
Sequence domains: Dynactin subunit 5
HOOK3 Chains: X, x
Molecule details ›
Chains: X, x
Length: 223 amino acids
Theoretical weight: 19 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
Dynactin Subunit 4 Chain: Y
Molecule details ›
Chain: Y
Length: 264 amino acids
Theoretical weight: 22.49 KDa
Source organism: Sus scrofa
Dynactin Subunit 1 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: 68 amino acids
Theoretical weight: 7.58 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A5G2QD80 (Residues: 1-68; Coverage: 17%)
Gene name: DCTN2
Dynactin subunit 2 Chain: b
Molecule details ›
Chain: b
Length: 90 amino acids
Theoretical weight: 10.15 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A5G2QD80 (Residues: 1-90; Coverage: 22%)
Gene name: DCTN2
Dynactin subunit 2 Chain: c
Molecule details ›
Chain: c
Length: 50 amino acids
Theoretical weight: 5.55 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SL58 (Residues: 1-50; Coverage: 13%)
Gene name: DCTN2
Dynactin subunit 2 Chain: d
Molecule details ›
Chain: d
Length: 29 amino acids
Theoretical weight: 3.24 KDa
Source organism: Sus scrofa
UniProt: Gene name: DCTN2
Cytoplasmic dynein 1 heavy chain 1 Chains: e, f, m, n
Molecule details ›
Chains: e, f, m, n
Length: 1455 amino acids
Theoretical weight: 168.32 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q14204 (Residues: 1-1455; Coverage: 31%)
Gene names: DHC1, DNCH1, DNCL, DNECL, DYHC, DYNC1H1, KIAA0325
Sequence domains:
Cytoplasmic dynein 1 intermediate chain 2 Chains: g, h, o, p
Molecule details ›
Chains: g, h, o, p
Length: 612 amino acids
Theoretical weight: 68.44 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q13409 (Residues: 1-638; Coverage: 96%)
Gene names: DNCI2, DNCIC2, DYNC1I2
Sequence domains:
Cytoplasmic dynein 1 light intermediate chain 2 Chains: i, j, q, r
Molecule details ›
Chains: i, j, q, r
Length: 492 amino acids
Theoretical weight: 54.17 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O43237 (Residues: 1-492; Coverage: 100%)
Gene names: DNCLI2, DYNC1LI2, LIC2
Sequence domains: Dynein light intermediate chain (DLIC)
Dynein light chain roadblock-type 1 Chains: k, l, s, t
Molecule details ›
Chains: k, l, s, t
Length: 96 amino acids
Theoretical weight: 10.93 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9NP97 (Residues: 1-96; Coverage: 100%)
Gene names: BITH, DNCL2A, DNLC2A, DYNLRB1, HSPC162, ROBLD1
Sequence domains: Roadblock/LC7 domain
Dynactin Subunit 1 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: 6.7Å
Relevant EMDB volumes: EMD-4177
Expression system: Spodoptera frugiperda

Quick links

Citations

20 review citations

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

2 mentions without citation

Bi-allelic Variants in DYNC1I2 Cause Syndromic Microcephaly with Intellectual Disability, Cerebral Malformations, and Dysmorphic Facial Features.
Ansar et al. (2019)
1 more