› 6dec

X-ray diffraction
4.6Å resolution

Crystal structure of Bos taurus Arp2/3 complex binding with C-terminus of Homo sapiens SPIN90

Released:
DOI: 10.2210/pdb6dec/pdb
PDB entry 6dec coloured by chain, front view.
PDB entry 6dec coloured by chain, side view.
PDB entry 6dec coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the nucleation-promoting factor SPIN90 bound to the actin filament nucleator Arp2/3 complex.
Luan Q, Liu SL, Helgeson LA, Nolen BJ
EMBO J 37 (2018)
PMID: 30322896

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero octamer (preferred)
monomeric
PDBe Complex ID:
PDB-CPX-108373 (preferred)
Entry contents:
10 distinct polypeptide molecules
Macromolecules (10 distinct):
Actin-related protein 3 Chains: A, H
Molecule details ›
Chains: A, H
Length: 418 amino acids
Theoretical weight: 47.43 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P61157 (Residues: 1-418; Coverage: 100%)
Gene names: ACTR3, ARP3
Sequence domains: Actin
Actin-related protein 2 Chains: B, I
Molecule details ›
Chains: B, I
Length: 394 amino acids
Theoretical weight: 44.82 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: A7MB62 (Residues: 1-394; Coverage: 100%)
Gene names: ACTR2, ARP2
Sequence domains: Actin
Actin-related protein 2/3 complex subunit 1B Chains: C, J
Molecule details ›
Chains: C, J
Length: 372 amino acids
Theoretical weight: 41.03 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q58CQ2 (Residues: 1-372; Coverage: 100%)
Gene name: ARPC1B
Sequence domains: WD domain, G-beta repeat
Actin-related protein 2/3 complex subunit 2 Chains: D, K
Molecule details ›
Chains: D, K
Length: 300 amino acids
Theoretical weight: 34.4 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q3MHR7 (Residues: 1-300; Coverage: 100%)
Gene name: ARPC2
Sequence domains: Arp2/3 complex, 34 kD subunit p34-Arc
Actin-related protein 2/3 complex subunit 3 Chains: E, L
Molecule details ›
Chains: E, L
Length: 178 amino acids
Theoretical weight: 20.57 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q3T035 (Residues: 1-178; Coverage: 100%)
Gene name: ARPC3
Sequence domains: ARP2/3 complex ARPC3 (21 kDa) subunit
Actin-related protein 2/3 complex subunit 4 Chains: F, N
Molecule details ›
Chains: F, N
Length: 168 amino acids
Theoretical weight: 19.7 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q148J6 (Residues: 1-168; Coverage: 100%)
Gene name: ARPC4
Sequence domains: ARP2/3 complex 20 kDa subunit (ARPC4)
Actin-related protein 2/3 complex subunit 5 Chains: G, O
Molecule details ›
Chains: G, O
Length: 151 amino acids
Theoretical weight: 16.25 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q3SYX9 (Residues: 1-151; Coverage: 100%)
Gene name: ARPC5
Sequence domains: ARP2/3 complex 16 kDa subunit (p16-Arc)
NCK-interacting protein with SH3 domain Chains: M, P
Molecule details ›
Chains: M, P
Length: 455 amino acids
Theoretical weight: 50.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NZQ3 (Residues: 269-722; Coverage: 63%)
Gene names: AF3P21, NCKIPSD, SPIN90
Sequence domains: SPIN90/Ldb17, leucine-rich domain
unidentified Chain: Q
Molecule details ›
Chain: Q
Length: 6 amino acids
Theoretical weight: 529 Da
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
unidentified Chain: R
Molecule details ›
Chain: R
Length: 9 amino acids
Theoretical weight: 784 Da
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

2 bound ligands:
Ligand CA 4 x CA
Ligand ATP 4 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 179.84Å b: 197.381Å c: 202.067Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.277 0.275 0.314
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Nucleation, stabilization, and disassembly of branched actin networks.
Gautreau et al. (2022)
14 other articles

3 mentions without citation

Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state.
Shaaban et al. (2020)
2 more