BMRB Entry 34874

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34874
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
Solution structure and chemical shift assignments for HMG-D Y12F mutant complexed to a 14:12 dA2 bulge DNA
Deposition date:
2023-11-02
Original release date:
2024-09-05
Authors:
Yang, J.; Hill, G.; Neuhaus, D.
Citation:

Citation: Hill, Guy; Yang, Ji-Chun; Easton, Laura; Cerdan, Rachel; McLaughlin, Stephen; Stott, Katherine; Travers, Andrew; Neuhaus, David. "A Single Interfacial Point Mutation Rescues Solution Structure Determination of the Complex of HMG-D with a DNA Bulge"  Chembiochem ., .-. (2024).
PubMed: 39145407

Assembly members:

Assembly members:
entity_1, polymer, 112 residues, 12426.941 Da.
entity_2, polymer, 14 residues, 4288.817 Da.
entity_3, polymer, 12 residues, 3662.404 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MSDKPKRPLSAFMLWLNSAR ESIKRENPGIKVTEVAKRGG ELWRAMKDKSEWEAKAAKAK DDYDRAVKEFEANGGSSAAN GGGAKKRAKPAKKVAKKSKK EESDEDDDDESE
entity_2: CGATATTAAGAGCC
entity_3: GGCTCAATATCG

Data sets:
Data typeCount
13C chemical shifts259
15N chemical shifts90
1H chemical shifts750

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_33

Entities:

Entity 1, unit_1 112 residues - 12426.941 Da.

1   METSERASPLYSPROLYSARGPROLEUSER
2   ALAPHEMETLEUTRPLEUASNSERALAARG
3   GLUSERILELYSARGGLUASNPROGLYILE
4   LYSVALTHRGLUVALALALYSARGGLYGLY
5   GLULEUTRPARGALAMETLYSASPLYSSER
6   GLUTRPGLUALALYSALAALALYSALALYS
7   ASPASPTYRASPARGALAVALLYSGLUPHE
8   GLUALAASNGLYGLYSERSERALAALAASN
9   GLYGLYGLYALALYSLYSARGALALYSPRO
10   ALALYSLYSVALALALYSLYSSERLYSLYS
11   GLUGLUSERASPGLUASPASPASPASPGLU
12   SERGLU

Entity 2, unit_2 14 residues - 4288.817 Da.

1   DCDGDADTDADTDTDADADG
2   DADGDCDC

Entity 3, unit_3 12 residues - 3662.404 Da.

1   DGDGDCDTDCDADADTDADT
2   DCDG

Samples:

sample_1: HMG-D Y12F, [U-13C; U-15N], 1.8 mM; DNA (5'-D(*CP*GP*AP*TP*AP*TP*TP*AP*AP*GP*AP*GP*CP*C)-3') 1.8 mM; DNA (5'-D(*GP*GP*CP*TP*CP*AP*AP*TP*AP*TP*CP*G)-3') 1.8 mM; sodium phosphate 10 mM; sodium chloride 20 mM; sodium azide 3 mM

sample_2: HMG-D Y12F, [U-13C; U-15N], 1.8 mM; DNA (5'-D(*CP*GP*AP*TP*AP*TP*TP*AP*AP*GP*AP*GP*CP*C)-3') 1.8 mM; DNA (5'-D(*GP*GP*CP*TP*CP*AP*AP*TP*AP*TP*CP*G)-3') 1.8 mM; sodium phosphate 10 mM; sodium chloride 20 mM; sodium azide 3 mM

sample_conditions_1: ionic strength: 83 mM; pH: 6.0; pressure: 1 atm; temperature: 300 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESY (mixing time = 60 ms)sample_1isotropicsample_conditions_1
2D 1H-1H NOESY (mixing time = 150 ms)sample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHANHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESY (mixing time = 150 ms)sample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphatic (mixing time = 150 ms)sample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromatic (mixing time = 150 ms)sample_1isotropicsample_conditions_1
2D [13C,15N]-filtered [1H-1H] NOESYsample_2isotropicsample_conditions_1
2D [13C,15N]-filtered [1H-1H] NOESYsample_2isotropicsample_conditions_1
13C-filtered 13C NOESY-HSQCsample_2isotropicsample_conditions_1

Software:

TopSpin v3.2 and 3.5, Bruker Biospin - processing

Sparky v3.115, Goddard - chemical shift assignment

X-PLOR NIH v2.28, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

Amber v11, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

  • Bruker AVANCE 500 MHz
  • Bruker AVANCE 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks