TAF4 (TATA box structure)

number condition
3.66528

max eigenvalue min eigenvalue
1.6511e-19_________3.568e-23

error computational SVD
1.3374e-19

PDB:7edx without TATA-box

number condition
3.5853

max eigenvalue min eigenvalue
1.6405e-19_________4.2642e-23

error computational SVD
1.385e-19

PDB:7eg8 TATA-box

Symbol: GTF2A2
Name: general transcription factor IIA, 2, 12kDa
Synonyms: HsT18745
_________ TFIIA

Symbol:TAF4
Name: TAF4 RNA polymerase II, TATA box binding protein
(TBP)-associated factor, 135kDa
Synonyms:TAF2C
_______________TAF2C1
_______________TAF4A
_______________TAFII130
_______________TAFII135

Mutations have been identified
that are in the region of
interacting polypeptide
chains during trimer formation
TAF4-T2AG-CH3
for two different structures: the presence of a DNA TATA box and the absence of a DNA TATA box

The structure of the trimer indicating the substitutions of amino acid residues in proteins

Difference in three-dimensional structures considering the presence and absence of the
DNA TATA box

Figure. 5. Structural overlay. visual comparison of three-dimensional structures 7edx and 7eg8.
As can be seen, the dimers coincide almost up to a couple of angstrems, however, the TAF4 alpha helix clearly has a different degree of immersion in the beta structures of the dimer.

PDB:7edx

PDB:7edx

PDB:7ed8

PDB:7ed8

PDB:7edx

PDB:7ed8

GTF2A2 PDB:7edx

TAF4 PDB:7edx

Figure 1.Dependence of RMSD(root-mean-square deviation) on the configuration number

Figure 2.Dependence of RMSD(root-mean-square deviation) on the configuration number

If an optimized cost function H for a specific PDB structure is found, then we consider that this structure is formed correctly and the following calculations are issued to find the local minimum. If an optimized cost function for a specific PDB structure is not found, then we consider that this structure is formed incorrectly, Fig.1-2.

Figure 3. Structure of biocomplex with
TATA-box.

Figure 4. Comparison of Structures with TATA-box and without TATA-box.

Table 1.

Figure 6. Calculation results for two different structures, taking into account the involved proteins.

Figure 7. List of file names for calculations used in the program.

Determination of the computational error of the SVD

Comparison of calculation results among themselves.