Instructor: Dr. Natalia Tretyakova, Ph.D. «hyperlink
"mailto:[email protected]"»
- 6-3432
PDB reference
correction and design Dr.chem., Ph.D. Aris
Kaksis, Associate Prof.
mailto:[email protected]
DNA
sequence specific binding Proteins
C-Jun
Proto Oncogene C-Fos Transcription Factor Ap-1 on 20 bp DNA
1FOS.pdb
--> B chain
5'-
T T
C T CC T A T G A C
T C A T CC A T -3'
chain B -->
<--- A chain
3'- A
G A
GG A T A C T G A G T A GG T A A-5' chain
A <---
Transcription
Activation Myod Helix-Loop-Helix
on double 14 bp DNA
1MDY.PDB
---> E chaine
5'-
T C A A C A GC
T G
T T G A- T
C A A C A GC
T G
T T G A-3'
chaine H --->
<--- F chaine
3'- A G T T G T CG
A C A
A C T -A G T T G T
CG A C A
A C T
-5' chaine G <---
Dna
Polymerase Beta E.C.2.7.7.7 Template-Primer 7 bp DNA fragment
2BPG.pdb
Mg2+ + 2',3'-DideoxyCytidine 5'-Triphosphate
DdCTP
<--- P chaine
3'- CCGCGGC-5'
chaine P <---
---> T chaine
5'-GGGCGCCG-3'
chaine T --->
DdCTP
9ICN.pdb 2 Na+ Tri
PO4
---> T chaine
5'-C
A T C
T G-3' chaine T --->
<--- P
chaine 3'-G
T A G A C-5' chaine P <---
1VAS.pdb EndoNuclease T4 on 13 bp DNA
fragment
A
<--- C chaine
3'-A gCgC
A CgCg
A T -5'
chain C <---
---> B
chaine 5'-A
T CgCg
T
gCgC T -3'
chain B --->
T
Met
Repressor-Operator METJ Biological Unit on 19 bp DNA one over
1CMA.PDB
---> G chaine
5'-
T T A g A Cg T
C T A g
A Cg T
C T A-3'
chain D --->
<--- H
chaine 3'-A T
C T gC
A g A T C
T gC A g A
T T -5' chain C <---
Arc Repressor-Operator on 21 bp DNA one
bp on
5' overhang
1PAR.PDB
<---
F chaine 3'-
T A
T C A T C
T C A Cg
A A
g A T A g
T AA-5' chain C <---
---> E chaine
5'-
T A
T A g T A g
A g
T gC
T T C T A T
C A T
-3' chain E --->
Purine
Repressor Hypoxanthine on single stranded 17 bases DNA
1PNR.PDB
ssDNA chaine 3'- T
gC T T T T gCAAAAgCAA-5'
Operator Or1 Phage 434 Cro on 20 bp DNA
fragment
3CRO.PDB
---> A chaine
5'-A A g
T A C A A A C T T T C
T T
g T A T -3'
<--- B chaine
3'- T C A T
g T T T
g A A
A g A A C A
T A
T -5'
Operator
Or3 BacterioPhage 434 Cro on 20 bp DNA fragment
1PER.pdb
<--- B chaine
3'- T C
A T g
T C A A A
A A g A A C A
T A
T -5'
---> A chaine
5'-A A g
T A C A g T T
T T T C
T T g T A T -3'
Engrailed Homeodomain Complex With 20 bp
DNA
fragment of
Fruit Fly
---> A chaine
5’-
T T T T
gCC A T
g T
A A
T T A CC T A A-3'
<--- B chaine 3’-A A A Cgg T A C A
T T A A T
gg A T T A-5'
Mouse
Musculus c-Myb binding 16 bp DNA fragment
1MSE.PDB
<--- A chaine
3'-
T | A C
A C A C
A g T C A A
T CC-5'
---> B chaine
5'-A |
T g T
g T g T C
A g T T A gg-3'
Mat Alpha2 HomeoDomain two units on 19
bp DNA
fragment
1APL.PDB
<--- A chaine 3’-CgC A C A
T T T A C
T T A A
T g T A CA-5'
---> B chaine
5’- T gCg T
g T
A A A
T g A A T T A C A T
g-3'
Telomere
24 bp DNA binding protein Rap1 two units
1IGN.PDB
C|
C|
---> E chaine
5'-CgCA CA CCCACAC ACC Ag
CTggTgTgTgggTgTgCg-3' D chaine
<--- F chaine
3'-gCgT gTgggTgTg
TggTC
gACCACACACCC ACACgC-5'
C chaine
C|
C|
Protein Prd paired 15 bp DNA fragment
1PDN.PDB
<--- A chaine 3'-CAg T T
ggC A C
T gCAA-5'
---> B chaine
5'-
TTgTC
A A CCg T g A Cg-3'
Antennapedia
HomeoDomain binding 16 bp DNA fragment
1AHD.PDB
---> A chaine
5'-g A A A gCC
A T T A g
A g-3'
<--- B chaine
3'-C T T T Cgg T A A T
C T C-5'
Site Specific
Recombinase g-d Resolvase With
34 Bp DNA
Cleavage Site
1GDT.PDB
---> C chaine
5'-gC
AgTgTCCgATAA TTTATAAA| T T A T Cgg A C A C T
g-3' D chaine
<--- F chaine
3'-g TCACAggCTATT|AAATATTT A A T A gCC T
g T g
A C-5'
E chaine
Binding
HIN recombinase with DNA 13 bp fragment and minor groove
---> B chaine
5’T-g- T-T-T- T-T-g- A- T- A- A-g-A
<--- C chaine 3’C-A-A-
A- A-
A-C- T- A- T-T-C-T