› 5nw4

Electron Microscopy
8.7Å resolution

Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2

Released:
DOI: 10.2210/pdb5nw4/pdb
PDB entry 5nw4 coloured by chain, front view.
PDB entry 5nw4 coloured by chain, side view.
PDB entry 5nw4 coloured by chain, top view.
Source organisms:
Primary publication:
Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated.
Zhang K, Foster HE, Rondelet A, Lacey SE, Bahi-Buisson N, Bird AW, Carter AP
Cell 169 1303-1314.e18 (2017)
PMID: 28602352
Related structures: EMD-3706

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 39-mer (preferred)
PDBe Complex ID:
PDB-CPX-102282 (preferred)
Entry contents:
28 distinct polypeptide molecules
Macromolecules (28 distinct):
dynein heavy chain Chain: B
Molecule details ›
Chain: B
Length: 889 amino acids
Theoretical weight: 75.68 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
dynein intermediate chain Chain: D
Molecule details ›
Chain: D
Length: 341 amino acids
Theoretical weight: 29.04 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
dynein intermediate chain Chain: C
Molecule details ›
Chain: C
Length: 350 amino acids
Theoretical weight: 29.8 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
dynein heavy chain Chain: A
Molecule details ›
Chain: A
Length: 922 amino acids
Theoretical weight: 78.48 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
dynein N-terminal dimerization domain Chain: 1
Molecule details ›
Chain: 1
Length: 125 amino acids
Theoretical weight: 10.66 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
dynein N-terminal dimerization domain Chain: 2
Molecule details ›
Chain: 2
Length: 124 amino acids
Theoretical weight: 10.57 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
Robl Chains: R, S
Molecule details ›
Chains: R, S
Length: 120 amino acids
Theoretical weight: 10.23 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
dynein light intermediate chain Chain: E
Molecule details ›
Chain: E
Length: 295 amino acids
Theoretical weight: 25.12 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
dynein light intermediate chain Chain: F
Molecule details ›
Chain: F
Length: 298 amino acids
Theoretical weight: 25.38 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
Alpha-centractin Chains: G, H, O, P, Q, T, U, W
Molecule details ›
Chains: G, H, O, P, Q, T, U, W
Length: 376 amino acids
Theoretical weight: 42.68 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F2Z5G5 (Residues: 1-310; Coverage: 89%)
Gene name: ACTR1A
Sequence domains: Actin
Actin, cytoplasmic 1 Chain: V
Molecule details ›
Chain: V
Length: 396 amino acids
Theoretical weight: 43.99 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A151MAL5 (Residues: 24-396; Coverage: 94%)
Gene name: Y1Q_0001713
Sequence domains: Actin
Actin-related protein 10 Chain: X
Molecule details ›
Chain: X
Length: 417 amino acids
Theoretical weight: 46.25 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LHK5 (Residues: 1-417; Coverage: 100%)
Gene names: ACTR10, ARP11
Sequence domains: Actin
F-actin-capping protein subunit alpha-1 Chain: Y
Molecule details ›
Chain: Y
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: Z
Molecule details ›
Chain: Z
Length: 293 amino acids
Theoretical weight: 33.06 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: D2JYW4 (Residues: 2-277; Coverage: 100%)
Gene name: CAPZB
Sequence domains: F-actin capping protein, beta subunit
dynactin shoulder complex Chain: a
Molecule details ›
Chain: a
Length: 571 amino acids
Theoretical weight: 48.61 KDa
Source organism: Sus scrofa
dynactin shoulder complex Chain: b
Molecule details ›
Chain: b
Length: 602 amino acids
Theoretical weight: 51.25 KDa
Source organism: Sus scrofa
dynactin shoulder complex Chains: c, d
Molecule details ›
Chains: c, d
Length: 130 amino acids
Theoretical weight: 11.08 KDa
Source organism: Sus scrofa
dynactin shoulder complex Chains: e, f
Molecule details ›
Chains: e, f
Length: 174 amino acids
Theoretical weight: 14.83 KDa
Source organism: Sus scrofa
Dynactin subunit 6 Chain: g
Molecule details ›
Chain: g
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: h
Molecule details ›
Chain: h
Length: 222 amino acids
Theoretical weight: 24.54 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q9BTE1 (Residues: 1-182; Coverage: 100%)
Gene name: DCTN5
Sequence domains: Dynactin subunit 5
dynactin pointed end p62 Chain: i
Molecule details ›
Chain: i
Length: 243 amino acids
Theoretical weight: 20.7 KDa
Source organism: Sus scrofa
p150 Chain: j
Molecule details ›
Chain: j
Length: 52 amino acids
Theoretical weight: 4.44 KDa
Source organism: Sus scrofa
Dynactin Chain: k
Molecule details ›
Chain: k
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: l
Molecule details ›
Chain: l
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: m
Molecule details ›
Chain: m
Length: 31 amino acids
Theoretical weight: 3.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0J9X299 (Residues: 1-31; Coverage: 100%)
Dynactin subunit 2 Chain: n
Molecule details ›
Chain: n
Length: 20 amino acids
Theoretical weight: 2.24 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A0J9X293 (Residues: 1-20; Coverage: 28%)
dynactin p150 Chain: o
Molecule details ›
Chain: o
Length: 53 amino acids
Theoretical weight: 4.53 KDa
Source organism: Sus scrofa
BICD2N Chains: 5, 6
Molecule details ›
Chains: 5, 6
Length: 275 amino acids
Theoretical weight: 23.42 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 8.7Å
Relevant EMDB volumes: EMD-3706
Expression system: Spodoptera frugiperda

Quick links

Citations

21 review citations

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

7 mentions without citation

Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated.
Zhang et al. (2017)
6 more