› 5cd4

X-ray diffraction
3.2Å resolution

The Type IE CRISPR Cascade complex from E. coli, with two assemblies in the asymmetric unit arranged back-to-back

Released:
DOI: 10.2210/pdb5cd4/pdb
PDB entry 5cd4 coloured by chain, front view.
PDB entry 5cd4 coloured by chain, side view.
PDB entry 5cd4 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli.
van Erp PB, Jackson RN, Carter J, Golden SM, Bailey S, Wiedenheft B
Nucleic Acids Res 43 8381-91 (2015)
PMID: 26243775

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160116 (preferred)
Entry contents:
5 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (6 distinct):
CRISPR system Cascade subunit CasE Chains: A, M
Molecule details ›
Chains: A, M
Length: 199 amino acids
Theoretical weight: 22.32 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: Q46897 (Residues: 1-199; Coverage: 100%)
Gene names: JW2726, b2756, cas6e, casE, ygcH
Sequence domains: CRISPR associated protein
Structure domains:
CRISPR system Cascade subunit CasC Chains: B, C, D, E, F, G, N, O, P, Q, R, S
Molecule details ›
Chains: B, C, D, E, F, G, N, O, P, Q, R, S
Length: 363 amino acids
Theoretical weight: 40.07 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: Q46899 (Residues: 1-363; Coverage: 100%)
Gene names: JW2728, b2758, cas4, casC, cse4, ygcJ
Sequence domains: CT1975-like protein
CRISPR system Cascade subunit CasD Chains: H, T
Molecule details ›
Chains: H, T
Length: 224 amino acids
Theoretical weight: 25.24 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: Q46898 (Residues: 1-224; Coverage: 100%)
Gene names: JW5844, b2757, cas5, casD, ygcI
Sequence domains: CRISPR-associated protein (Cas_Cas5)
Structure domains: Alpha-Beta Plaits
CRISPR system Cascade subunit CasA Chains: I, U
Molecule details ›
Chains: I, U
Length: 502 amino acids
Theoretical weight: 55.96 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: Q46901 (Residues: 1-502; Coverage: 100%)
Gene names: JW2730, b2760, casA, cse1, ygcL
Sequence domains: CRISPR-associated protein Cse1 (CRISPR_cse1)
CRISPR system Cascade subunit CasB Chains: J, K, V, W
Molecule details ›
Chains: J, K, V, W
Length: 165 amino acids
Theoretical weight: 19.23 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P76632 (Residues: 1-160; Coverage: 100%)
Gene names: JW2729, b2759, casB, cse2, ygcK
Sequence domains: CRISPR-associated protein Cse2 (CRISPR_cse2)
Structure domains: CRISPR-associated protein Cse2
crRNA Chains: L, X
Molecule details ›
Chains: L, X
Length: 61 nucleotides
Theoretical weight: 19.68 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
1 modified residue:
Ligand 23G 2 x 23G

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 105.99Å b: 244.8Å c: 426.74Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.212 0.25
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering.
Wright et al. (2016)
10 more

5 mentions without citation

UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Goddard et al. (2018)
4 more