BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 4141

Title: vnd/NK-2 Homeodomain DNA Complex Protein 1H, 13C, and 15N Chemical Shifts and HNHA Coupling Constant   PubMed: 10356327

Authors: Gruschus, James; Tsao, Desiree; Wang, Lan-Hsiang; Nirenberg, Marshall; Ferretti, James

Citation: Gruschus, James; Tsao, Desiree; Wang, Lan-Hsiang; Nirenberg, Marshall; Ferretti, James. "The three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex by NMR spectroscopy"  J. Mol. Biol. 289, 529-545 (1999).

Assembly members:
vnd/NK-2 homeodomain, polymer, 77 residues, Formula weight is not available
(+)5'TGTGTCAAGTGGCTGT, polymer, 16 residues, Formula weight is not available
(-)5'ACAGCCACTTGACACAA, polymer, 16 residues, Formula weight is not available

Natural source:   Common Name: fruit fly   Taxonomy ID: 7227   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Drosophila melanogaster

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
vnd/NK-2 homeodomain: ASDGLPNKKRKRRVLFTKAQ TYELERRFRQQRYLSAPERE HLASLIRLTPTQVKIWFQNH RYKTKRAQNEKGYEGHP
(+)5'TGTGTCAAGTGGCTGT: TGTGTCAAGTGGCTGT
(-)5'ACAGCCACTTGACACAA: ACAGCCACTTGACACAA

Data typeCount
13C chemical shifts291
15N chemical shifts100
1H chemical shifts904
31P chemical shifts18
coupling constants53

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1vnd/NK-2 homeodomain1
2DNA duplex (+) strand2
3DNA duplex (-) strand3

Entities:

Entity 1, vnd/NK-2 homeodomain 77 residues - Formula weight is not available

1   ALASERASPGLYLEUPROASNLYSLYSARG
2   LYSARGARGVALLEUPHETHRLYSALAGLN
3   THRTYRGLULEUGLUARGARGPHEARGGLN
4   GLNARGTYRLEUSERALAPROGLUARGGLU
5   HISLEUALASERLEUILEARGLEUTHRPRO
6   THRGLNVALLYSILETRPPHEGLNASNHIS
7   ARGTYRLYSTHRLYSARGALAGLNASNGLU
8   LYSGLYTYRGLUGLYHISPRO

Entity 2, DNA duplex (+) strand 16 residues - Formula weight is not available

1   DTDGDTDGDTDCDADADGDT
2   DGDGDCDTDGDT

Entity 3, DNA duplex (-) strand 16 residues - Formula weight is not available

1   DADCDADGDCDCDADCDTDT
2   DGDADCDADCDADA

Samples:

sample_1: vnd/NK-2 homeodomain, [U13C; U-15N], 1.5 – 2.0 mM; (+)5'TGTGTCAAGTGGCTGT1.425 – 1.9 mM; (-)5'ACAGCCACTTGACACAA1.425 – 1.9 mM; NaCl 80 mM; D2O 10%; H2O 90%

sample_2: vnd/NK-2 homeodomain, [U-15N], 1.5 – 2.0 mM; (+)5'TGTGTCAAGTGGCTGT1.425 – 1.9 mM; (-)5'ACAGCCACTTGACACAA1.425 – 1.9 mM; NaCl 80 mM; D2O 10%; H2O 90%

sample_3: vnd/NK-2 homeodomain, [U-13C; U-15N], 1.5 – 2.0 mM; (+)5'TGTGTCAAGTGGCTGT1.425 – 1.9 mM; (-)5'ACAGCCACTTGACACAA1.425 – 1.9 mM; NaCl 80 mM; D2O 100%

cond_1: ionic strength: 0.08 M; pH: 6.0; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
1H-15N NOESY-HMQCnot availablenot availablecond_1
1H-13C NOESY-HSQCnot availablenot availablecond_1
1H-15N TOCSYnot availablenot availablecond_1
1H-15N HMQC-Jnot availablenot availablecond_1
15N experiments in H2Onot availablenot availablecond_1
13C experiments in D2Onot availablenot availablecond_1

Software:

NMRPipe - Fourier transformation

NMR spectrometers:

  • Bruker AMX 600 MHz

Related Database Links:

BMRB 4368
PDB
EMBL CAA21410 CAA60619
GB AAA28617 AAB34960 AAF45521 ABI30961 ADJ13174
REF NP_001036253 NP_476786 XP_001354499 XP_001982405 XP_001992446
SP P22808