› 1jfi

X-ray diffraction
2.62Å resolution

Crystal Structure of the NC2-TBP-DNA Ternary Complex

Released:
DOI: 10.2210/pdb1jfi/pdb
PDB entry 1jfi coloured by chain, front view.
PDB entry 1jfi coloured by chain, side view.
PDB entry 1jfi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex.
Kamada K, Shu F, Chen H, Malik S, Stelzer G, Roeder RG, Meisterernst M, Burley SK
Cell 106 71-81 (2001)
PMID: 11461703

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114001 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (5 distinct):
Dr1-associated corepressor Chain: A
Molecule details ›
Chain: A
Length: 98 amino acids
Theoretical weight: 10.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q14919 (Residues: 1-77; Coverage: 38%)
Gene name: DRAP1
Sequence domains: Histone-like transcription factor (CBF/NF-Y) and archaeal histone
Structure domains: Histone, subunit A
Protein Dr1 Chain: B
Molecule details ›
Chain: B
Length: 179 amino acids
Theoretical weight: 19.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q01658 (Residues: 1-176; Coverage: 100%)
Gene name: DR1
Sequence domains: Histone-like transcription factor (CBF/NF-Y) and archaeal histone
Structure domains: Histone, subunit A
TATA-box-binding protein Chain: C
Molecule details ›
Chain: C
Length: 185 amino acids
Theoretical weight: 20.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P20226 (Residues: 159-339; Coverage: 53%)
Gene names: GTF2D1, TBP, TF2D, TFIID
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
Structure domains: TATA-Binding Protein
5'-D(*TP*TP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*CP*C)-3' Chain: D
Molecule details ›
Chain: D
Length: 19 nucleotides
Theoretical weight: 5.84 KDa
5'-D(*G*GP*AP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*AP*A)-3' Chain: E
Molecule details ›
Chain: E
Length: 19 nucleotides
Theoretical weight: 5.8 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2221
Unit cell:
a: 76.684Å b: 119.075Å c: 155.076Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.239 0.233 0.277
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

15 review citations

The general transcription machinery and general cofactors.
Thomas et al. (2006)
14 more

15 mentions without citation

Structure and mechanism of the RNA polymerase II transcription machinery.
Schier et al. (2020)
14 more