› 6uep

X-ray diffraction
2.05Å resolution

Structure of A. thaliana TBP bound to a DNA site with a C-C mismatch

Released:
DOI: 10.2210/pdb6uep/pdb
PDB entry 6uep coloured by chain, front view.
PDB entry 6uep coloured by chain, side view.
PDB entry 6uep coloured by chain, top view.
Source organisms:
Primary publication:
DNA mismatches reveal conformational penalties in protein-DNA recognition.
Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordân R
Nature 587 291-296 (2020)
PMID: 33087930

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120691 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
TATA-box-binding protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 219 amino acids
Theoretical weight: 24.51 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: P28147 (Residues: 1-200; Coverage: 100%)
Gene names: At3g13445, MRP15.10, TBP1
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 14 nucleotides
Theoretical weight: 4.31 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*GP*CP*CP*CP*CP*TP*TP*TP*AP*TP*AP*GP*C)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 14 nucleotides
Theoretical weight: 4.21 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand FMT 3 x FMT
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: C2
Unit cell:
a: 113.648Å b: 46.654Å c: 146.302Å
α: 90° β: 95.51° γ: 90°
R-values:
R R work R free
0.172 0.172 0.192
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Adaptive homeostasis and the p53 isoform network.
Mehta et al. (2021)
4 more

1 mention without citation

DNA mismatches reveal conformational penalties in protein-DNA recognition.
Afek et al. (2020)