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BMRB: 4141

1NK2

vnd/NK-2 Homeodomain DNA Complex Protein 1H, 13C, and 15N Chemical Shifts and HNHA Coupling Constant

Authors

Gruschus, J.M., Tsao, D.H.H., Wang, L., Nirenberg, M., Ferretti, J.A.

Assembly

vnd/NK-2 homeodomain DNA complex

Entity

1. vnd/NK-2 homeodomain (polymer, Thiol state: not present), 77 monomers, 9352.561 Da Detail

ASDGLPNKKR KRRVLFTKAQ TYELERRFRQ QRYLSAPERE HLASLIRLTP TQVKIWFQNH RYKTKRAQNE KGYEGHP

2. (+)5'TGTGTCAAGTGGCTGT (polymer, Thiol state: not present), 16 monomers, 5023.183 Da Detail

TGTGTCAAGT GGCTGT

3. (-)5'ACAGCCACTTGACACAA (polymer, Thiol state: not present), 17 monomers, 5212.350 Da Detail

ACAGCCACTT GACACAA

Total weight

19588.094 Da

Max. entity weight

9352.561 Da

Source organism

Drosophila melanogaster

Exptl. method

NMR

Refine. method

DISTANCE GEOMETRY/ SIMULATED ANNEALING

Data set

assigned_chemical_shifts, coupling_constants

Chem. Shift Complete1

Sequence coverage: 70.0 %, Completeness: 68.2 %, Completeness (bb): 53.6 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	68.2 % (912 of 1338)	62.0 % (527 of 850)	81.7 % (304 of 372)	97.6 % (81 of 83)	0.0 % (0 of 33)
Backbone	53.6 % (385 of 718)	39.6 % (152 of 384)	71.1 % (162 of 228)	97.3 % (71 of 73)	0.0 % (0 of 33)
Sidechain	86.6 % (601 of 694)	80.5 % (375 of 466)	99.1 % (216 of 218)	100.0 % (10 of 10)
Aromatic	56.6 % (86 of 152)	39.4 % (43 of 109)	100.0 % (42 of 42)	100.0 % (1 of 1)
Methyl	88.9 % (64 of 72)	80.0 % (32 of 40)	100.0 % (32 of 32)

1. vnd/NK-2 homeodomain

ASDGLPNKKR KRRVLFTKAQ TYELERRFRQ QRYLSAPERE HLASLIRLTP TQVKIWFQNH RYKTKRAQNE KGYEGHP

2. (+)5'TGTGTCAAGTGGCTGT

TGTGTCAAGT GGCTGT

3. (-)5'ACAGCCACTTGACACAA

ACAGCCACTT GACACAA

Show sample condition

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

Chem. Shift Complete2

Sequence coverage: 28.2 %, Completeness: 42.8 %, Completeness (bb): 38.2 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	42.8 % (1145 of 2676)	40.7 % (692 of 1700)	46.6 % (347 of 744)	56.6 % (94 of 166)	18.2 % (12 of 66)
Backbone	38.2 % (549 of 1436)	33.3 % (256 of 768)	43.2 % (197 of 456)	57.5 % (84 of 146)	18.2 % (12 of 66)
Sidechain	49.1 % (682 of 1388)	46.8 % (436 of 932)	54.1 % (236 of 436)	50.0 % (10 of 20)
Aromatic	38.2 % (116 of 304)	33.5 % (73 of 218)	50.0 % (42 of 84)	50.0 % (1 of 2)
Methyl	52.8 % (76 of 144)	51.2 % (41 of 80)	54.7 % (35 of 64)

1. vnd/NK-2 homeodomain

ASDGLPNKKR KRRVLFTKAQ TYELERRFRQ QRYLSAPERE HLASLIRLTP TQVKIWFQNH RYKTKRAQNE KGYEGHP

2. (+)5'TGTGTCAAGTGGCTGT

TGTGTCAAGT GGCTGT

3. (-)5'ACAGCCACTTGACACAA

ACAGCCACTT GACACAA

Show sample condition

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

Chem. Shift Complete3

Sequence coverage: 31.8 %, Completeness: 35.2 %, Completeness (bb): 33.1 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	35.2 % (1413 of 4014)	35.5 % (904 of 2550)	34.4 % (384 of 1116)	43.0 % (107 of 249)	18.2 % (18 of 99)
Backbone	33.1 % (714 of 2154)	32.0 % (369 of 1152)	33.6 % (230 of 684)	44.3 % (97 of 219)	18.2 % (18 of 99)
Sidechain	38.1 % (794 of 2082)	38.3 % (535 of 1398)	38.1 % (249 of 654)	33.3 % (10 of 30)
Aromatic	33.6 % (153 of 456)	33.6 % (110 of 327)	33.3 % (42 of 126)	33.3 % (1 of 3)
Methyl	38.9 % (84 of 216)	38.3 % (46 of 120)	39.6 % (38 of 96)

1. vnd/NK-2 homeodomain

ASDGLPNKKR KRRVLFTKAQ TYELERRFRQ QRYLSAPERE HLASLIRLTP TQVKIWFQNH RYKTKRAQNE KGYEGHP

2. (+)5'TGTGTCAAGTGGCTGT

TGTGTCAAGT GGCTGT

3. (-)5'ACAGCCACTTGACACAA

ACAGCCACTT GACACAA

Show sample condition

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 1NK2, Strand ID: P Detail

Coupling constant

53 J values in 1 lists
Field strength (¹H) 600 MHz, Temperature 308 (±0.2) K, pH 6.0 (±0.2) Detail

Release date

2001-03-06

Citation 1

The three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex by NMR spectroscopy
Gruschus, J.M., Tsao, D.H.H., Wang, L., Nirenberg, M., Ferretti, J.A.
J. Mol. Biol. (1999), 289, 529-545, PubMed 10356327 , DOI 10.1006/jmbi.1999.2774 , Abstract

Show more 3 citaions

Citation 2

Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity
Gruschus, J.M., Tsao, D.H., Wang, L.H., Nirenberg, M., Ferretti, J.A.
Biochemistry (1997), 36, 5372-5380, PubMed 9154919 , DOI 10.1021/bi9620060 , Abstract

Citation 3

The three-dimensional solution structure of the NK-2 homeodomain from Drosophila
Tsao, D.H., Gruschus, J.M., Wang, L.H., Nirenberg, M., Ferretti, J.A.
J. Mol. Biol. (1995), 251, 297-307, PubMed 7643404 , DOI 10.1006/jmbi.1995.0435 , Abstract

Citation 4

Elongation of helix III of the NK-2 homeodomain upon binding to DNA: a secondary structure study by NMR
Tsao, D.H., Gruschus, J.M., Wang, L.H., Nirenberg, M., Ferretti, J.A.
Biochemistry (1994), 33, 15053-15060, PubMed 7999763 , DOI 10.1021/bi00254a014 , Abstract

Hide non-primary 3 citaions

Related entities 1. vnd/NK-2 homeodomain, : 1 : 2 : 3 : 133 entities Detail

Experiments performed 6 experiments Detail

1 1H-15N NOESY-HMQC

Instrument

Model Bruker AMX (600 MHz)

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

2 1H-13C NOESY-HSQC

Instrument

Model Bruker AMX (600 MHz)

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

3 1H-15N TOCSY

Instrument

Model Bruker AMX (600 MHz)

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

4 1H-15N HMQC-J

Instrument

Model Bruker AMX (600 MHz)

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

5 15N experiments in H2O

Instrument

Model Bruker AMX (600 MHz)

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

6 13C experiments in D2O

Instrument

Model Bruker AMX (600 MHz)

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

nullKeywords dna-binding protein, embryonic development, homeodomain

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Found 1 Document (1.887 seconds)

BMRB: 4141

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. vnd/NK-2 homeodomain, : 1 : 2 : 3 : 133 entities Detail

Experiments performed 6 experiments Detail

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