› 6jw2

X-ray diffraction
3.03Å resolution

Universal RVD R* accommodates 5hmC via water-mediated interactions

Released:
DOI: 10.2210/pdb6jw2/pdb
PDB entry 6jw2 coloured by chain, front view.
PDB entry 6jw2 coloured by chain, side view.
PDB entry 6jw2 coloured by chain, top view.
Source organisms:
Primary publication:
Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors.
Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J
J Mol Biol 432 1035-1047 (2020)
PMID: 31863750

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120106 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Avirulence protein AvrBs3 Chains: A, B, E, H
Molecule details ›
Chains: A, B, E, H
Length: 498 amino acids
Theoretical weight: 51.82 KDa
Source organism: Xanthomonas campestris pv. armoraciae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q3ZD72 (Residues: 231-724; Coverage: 51%)
Gene name: hax3
Sequence domains: TAL effector repeat
DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5HC)P*GP*CP*GP*TP*CP*TP*CP*T)-3') Chains: C, F, I, K
Molecule details ›
Chains: C, F, I, K
Length: 17 nucleotides
Theoretical weight: 5.13 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3') Chains: D, G, J, L
Molecule details ›
Chains: D, G, J, L
Length: 17 nucleotides
Theoretical weight: 5.32 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5HC 4 x 5HC

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P21
Unit cell:
a: 94.517Å b: 93.776Å c: 167.749Å
α: 90° β: 102.66° γ: 90°
R-values:
R R work R free
0.238 0.237 0.261
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

TALENs-an indispensable tool in the era of CRISPR: a mini review.
Bhardwaj et al. (2021)
1 other article

1 mention without citation

Structural mechanism for amino acid-dependent Rag GTPase nucleotide state switching by SLC38A9.
Fromm et al. (2020)