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BMRB: 7097

2GLO

DNA recognition by the Brinker nuclear repressor - an extreme case of the coupling between binding and folding

Authors

Cordier, F., Hartmann, B., Rogowski, M., Affolter, M., Grzesiek, S.

Assembly

brinker CG9653-PA/DNA Complex

Entity

1. brinker CG9653-PA (polymer, Thiol state: all free), 59 monomers, 7047.835 Da Detail

GSRRIFTPHF KLQVLESYRN DNDCKGNQRA TARKYNIHRR QIQKWLQCES NLRSSVANN

2. 5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3' (polymer, Thiol state: not present), 12 monomers, 3750.389 Da Detail

TGAGGCGTCA AC

3. 5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3' (polymer, Thiol state: not present), 12 monomers, 3701.351 Da Detail

GTTGACGCCT CA

Total weight

14499.574 Da

Max. entity weight

7047.835 Da

Source organism

Drosophila melanogaster

Exptl. method

NMR

Refine. method

torsion angle dynamics; distance geometry

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 71.1 %, Completeness: 72.7 %, Completeness (bb): 66.3 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	72.7 % (697 of 959)	60.0 % (373 of 622)	95.9 % (255 of 266)	97.2 % (69 of 71)
Backbone	66.3 % (345 of 520)	40.4 % (116 of 287)	98.3 % (172 of 175)	98.3 % (57 of 58)
Sidechain	82.5 % (409 of 496)	76.7 % (257 of 335)	94.6 % (140 of 148)	92.3 % (12 of 13)
Aromatic	38.5 % (40 of 104)	26.3 % (20 of 76)	70.4 % (19 of 27)	100.0 % (1 of 1)
Methyl	90.2 % (46 of 51)	82.1 % (23 of 28)	100.0 % (23 of 23)

1. brinker CG9653-PA

GSRRIFTPHF KLQVLESYRN DNDCKGNQRA TARKYNIHRR QIQKWLQCES NLRSSVANN

2. 5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3'

TGAGGCGTCA AC

3. 5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3'

GTTGACGCCT CA

Show sample condition

Sample

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	brinker CG9653-PA	[U-15N]	1 mM
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
4	NaCl		10 mM
5	potassium phosphate		5 mM
6	TCEP		5 mM
7	NaN3		0.02 %
8	H2O		95 %
9	D2O		5 %

Chem. Shift Complete2

Sequence coverage: 19.3 %, Completeness: 42.0 %, Completeness (bb): 39.2 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	42.0 % (805 of 1918)	37.2 % (463 of 1244)	50.4 % (268 of 532)	52.1 % (74 of 142)
Backbone	39.2 % (408 of 1040)	29.1 % (167 of 574)	51.4 % (180 of 350)	52.6 % (61 of 116)
Sidechain	46.0 % (456 of 992)	44.2 % (296 of 670)	49.7 % (147 of 296)	50.0 % (13 of 26)
Aromatic	36.1 % (75 of 208)	32.2 % (49 of 152)	44.4 % (24 of 54)	100.0 % (2 of 2)
Methyl	47.1 % (48 of 102)	44.6 % (25 of 56)	50.0 % (23 of 46)

1. brinker CG9653-PA

GSRRIFTPHF KLQVLESYRN DNDCKGNQRA TARKYNIHRR QIQKWLQCES NLRSSVANN

2. 5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3'

TGAGGCGTCA AC

3. 5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3'

GTTGACGCCT CA

Show sample condition

Sample

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	brinker CG9653-PA	[U-15N]	1 mM
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
4	NaCl		10 mM
5	potassium phosphate		5 mM
6	TCEP		5 mM
7	NaN3		0.02 %
8	H2O		95 %
9	D2O		5 %

Chem. Shift Complete3

Sequence coverage: 22.9 %, Completeness: 32.6 %, Completeness (bb): 31.0 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	32.6 % (939 of 2877)	30.5 % (570 of 1866)	36.2 % (289 of 798)	37.6 % (80 of 213)
Backbone	31.0 % (484 of 1560)	25.8 % (222 of 861)	37.1 % (195 of 525)	38.5 % (67 of 174)
Sidechain	34.9 % (519 of 1488)	34.6 % (348 of 1005)	35.6 % (158 of 444)	33.3 % (13 of 39)
Aromatic	31.4 % (98 of 312)	31.6 % (72 of 228)	29.6 % (24 of 81)	66.7 % (2 of 3)
Methyl	33.3 % (51 of 153)	33.3 % (28 of 84)	33.3 % (23 of 69)

1. brinker CG9653-PA

GSRRIFTPHF KLQVLESYRN DNDCKGNQRA TARKYNIHRR QIQKWLQCES NLRSSVANN

2. 5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3'

TGAGGCGTCA AC

3. 5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3'

GTTGACGCCT CA

Show sample condition

Sample

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	brinker CG9653-PA	[U-15N]	1 mM
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
4	NaCl		10 mM
5	potassium phosphate		5 mM
6	TCEP		5 mM
7	NaN3		0.02 %
8	H2O		95 %
9	D2O		5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2GLO, Strand ID: A Detail

Release date

2006-09-21

Citation

DNA recognition by the brinker repressor--an extreme case of coupling between binding and folding
Cordier, F., Hartmann, B., Rogowski, M., Affolter, M., Grzesiek, S.
J. Mol. Biol. (2006), 361, 659-672, PubMed 16876822 , DOI 10.1016/j.jmb.2006.06.045 , Abstract

Related entities 1. brinker CG9653-PA, : 1 : 1 : 9 entities Detail

Experiments performed 9 experiments Detail

1 3D 15N-separated NOESY

Instrument

Model Bruker DRX (800 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	brinker CG9653-PA	[U-15N]	1 mM
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
4	NaCl		10 mM
5	potassium phosphate		5 mM
6	TCEP		5 mM
7	NaN3		0.02 %
8	H2O		95 %
9	D2O		5 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
10	brinker CG9653-PA	[U-13C; U-15N]	1 mM
11	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
12	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
13	NaCl		10 mM
14	potassium phosphate		5 mM
15	TCEP		5 mM
16	NaN3		0.02 %
17	H2O		95 %
18	D2O		5 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
19	brinker CG9653-PA	[U-13C; U-15N]	0.35 mM
20	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		0.35 mM
21	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		0.35 mM
22	NaCl		10 mM
23	potassium phosphate		20 mM
24	DTT		2 mM
25	NaN3		0.02 %
26	Pf1-phages		25 mg/mL
27	H2O		95 %
28	D2O		5 %

2 3D 13C-separated NOESY

Instrument

Model Bruker DRX (800 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	brinker CG9653-PA	[U-15N]	1 mM
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
4	NaCl		10 mM
5	potassium phosphate		5 mM
6	TCEP		5 mM
7	NaN3		0.02 %
8	H2O		95 %
9	D2O		5 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
10	brinker CG9653-PA	[U-13C; U-15N]	1 mM
11	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
12	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
13	NaCl		10 mM
14	potassium phosphate		5 mM
15	TCEP		5 mM
16	NaN3		0.02 %
17	H2O		95 %
18	D2O		5 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
19	brinker CG9653-PA	[U-13C; U-15N]	0.35 mM
20	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		0.35 mM
21	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		0.35 mM
22	NaCl		10 mM
23	potassium phosphate		20 mM
24	DTT		2 mM
25	NaN3		0.02 %
26	Pf1-phages		25 mg/mL
27	H2O		95 %
28	D2O		5 %

3 3D dq-HNHA

Instrument

Model Bruker DRX (800 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	brinker CG9653-PA	[U-15N]	1 mM
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
4	NaCl		10 mM
5	potassium phosphate		5 mM
6	TCEP		5 mM
7	NaN3		0.02 %
8	H2O		95 %
9	D2O		5 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
10	brinker CG9653-PA	[U-13C; U-15N]	1 mM
11	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
12	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
13	NaCl		10 mM
14	potassium phosphate		5 mM
15	TCEP		5 mM
16	NaN3		0.02 %
17	H2O		95 %
18	D2O		5 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
19	brinker CG9653-PA	[U-13C; U-15N]	0.35 mM
20	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		0.35 mM
21	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		0.35 mM
22	NaCl		10 mM
23	potassium phosphate		20 mM
24	DTT		2 mM
25	NaN3		0.02 %
26	Pf1-phages		25 mg/mL
27	H2O		95 %
28	D2O		5 %

4 3D dq-HAHB

Instrument

Model Bruker DRX (800 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	brinker CG9653-PA	[U-15N]	1 mM
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
4	NaCl		10 mM
5	potassium phosphate		5 mM
6	TCEP		5 mM
7	NaN3		0.02 %
8	H2O		95 %
9	D2O		5 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
10	brinker CG9653-PA	[U-13C; U-15N]	1 mM
11	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
12	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
13	NaCl		10 mM
14	potassium phosphate		5 mM
15	TCEP		5 mM
16	NaN3		0.02 %
17	H2O		95 %
18	D2O		5 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
19	brinker CG9653-PA	[U-13C; U-15N]	0.35 mM
20	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		0.35 mM
21	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		0.35 mM
22	NaCl		10 mM
23	potassium phosphate		20 mM
24	DTT		2 mM
25	NaN3		0.02 %
26	Pf1-phages		25 mg/mL
27	H2O		95 %
28	D2O		5 %

5 2D HNCG

Instrument

Model Bruker DRX (800 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	brinker CG9653-PA	[U-15N]	1 mM
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
4	NaCl		10 mM
5	potassium phosphate		5 mM
6	TCEP		5 mM
7	NaN3		0.02 %
8	H2O		95 %
9	D2O		5 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
10	brinker CG9653-PA	[U-13C; U-15N]	1 mM
11	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
12	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
13	NaCl		10 mM
14	potassium phosphate		5 mM
15	TCEP		5 mM
16	NaN3		0.02 %
17	H2O		95 %
18	D2O		5 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
19	brinker CG9653-PA	[U-13C; U-15N]	0.35 mM
20	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		0.35 mM
21	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		0.35 mM
22	NaCl		10 mM
23	potassium phosphate		20 mM
24	DTT		2 mM
25	NaN3		0.02 %
26	Pf1-phages		25 mg/mL
27	H2O		95 %
28	D2O		5 %

6 2D HN(CO)CG

Instrument

Model Bruker DRX (800 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	brinker CG9653-PA	[U-15N]	1 mM
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
4	NaCl		10 mM
5	potassium phosphate		5 mM
6	TCEP		5 mM
7	NaN3		0.02 %
8	H2O		95 %
9	D2O		5 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
10	brinker CG9653-PA	[U-13C; U-15N]	1 mM
11	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
12	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
13	NaCl		10 mM
14	potassium phosphate		5 mM
15	TCEP		5 mM
16	NaN3		0.02 %
17	H2O		95 %
18	D2O		5 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
19	brinker CG9653-PA	[U-13C; U-15N]	0.35 mM
20	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		0.35 mM
21	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		0.35 mM
22	NaCl		10 mM
23	potassium phosphate		20 mM
24	DTT		2 mM
25	NaN3		0.02 %
26	Pf1-phages		25 mg/mL
27	H2O		95 %
28	D2O		5 %

7 2D 13C-selected/12C,14N-selected NOESY

Instrument

Model Bruker DRX (800 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	brinker CG9653-PA	[U-15N]	1 mM
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
4	NaCl		10 mM
5	potassium phosphate		5 mM
6	TCEP		5 mM
7	NaN3		0.02 %
8	H2O		95 %
9	D2O		5 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
10	brinker CG9653-PA	[U-13C; U-15N]	1 mM
11	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
12	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
13	NaCl		10 mM
14	potassium phosphate		5 mM
15	TCEP		5 mM
16	NaN3		0.02 %
17	H2O		95 %
18	D2O		5 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
19	brinker CG9653-PA	[U-13C; U-15N]	0.35 mM
20	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		0.35 mM
21	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		0.35 mM
22	NaCl		10 mM
23	potassium phosphate		20 mM
24	DTT		2 mM
25	NaN3		0.02 %
26	Pf1-phages		25 mg/mL
27	H2O		95 %
28	D2O		5 %

8 DSSE

Instrument

Model Bruker DRX (800 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	brinker CG9653-PA	[U-15N]	1 mM
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
4	NaCl		10 mM
5	potassium phosphate		5 mM
6	TCEP		5 mM
7	NaN3		0.02 %
8	H2O		95 %
9	D2O		5 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
10	brinker CG9653-PA	[U-13C; U-15N]	1 mM
11	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
12	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
13	NaCl		10 mM
14	potassium phosphate		5 mM
15	TCEP		5 mM
16	NaN3		0.02 %
17	H2O		95 %
18	D2O		5 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
19	brinker CG9653-PA	[U-13C; U-15N]	0.35 mM
20	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		0.35 mM
21	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		0.35 mM
22	NaCl		10 mM
23	potassium phosphate		20 mM
24	DTT		2 mM
25	NaN3		0.02 %
26	Pf1-phages		25 mg/mL
27	H2O		95 %
28	D2O		5 %

9 J-modulated-13C-HSQC

Instrument

Model Bruker DRX (800 MHz)

Sample #1

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
1	brinker CG9653-PA	[U-15N]	1 mM
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
4	NaCl		10 mM
5	potassium phosphate		5 mM
6	TCEP		5 mM
7	NaN3		0.02 %
8	H2O		95 %
9	D2O		5 %

Sample #2

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
10	brinker CG9653-PA	[U-13C; U-15N]	1 mM
11	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		1 mM
12	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		1 mM
13	NaCl		10 mM
14	potassium phosphate		5 mM
15	TCEP		5 mM
16	NaN3		0.02 %
17	H2O		95 %
18	D2O		5 %

Sample #3

Pressure 1 atm, Temperature 298 K, pH 5.8

#	Name	Isotope labeling	Concentration
19	brinker CG9653-PA	[U-13C; U-15N]	0.35 mM
20	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'		0.35 mM
21	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'		0.35 mM
22	NaCl		10 mM
23	potassium phosphate		20 mM
24	DTT		2 mM
25	NaN3		0.02 %
26	Pf1-phages		25 mg/mL
27	H2O		95 %
28	D2O		5 %

nullKeywords HELIX-TURN-HELIX MOTIF, PROTEIN-DNA COMPLEX

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Found 1 Document (6.99 seconds)

BMRB: 7097

Sample

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Related entities 1. brinker CG9653-PA, : 1 : 1 : 9 entities Detail

Experiments performed 9 experiments Detail

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