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BMRB: 19511

2ME0

NMR Structure of the homeodomain transcription factor Gbx1 from Homo sapiens solved in the presence of the DNA sequence CGACTAATTAGTCG

Authors

Proudfoot, A., Serrano, P., Geralt, M., Wuthrich, K.

Assembly

homeodomain transcription factor Gbx1

Entity

1. Gbx1 (polymer, Thiol state: all free), 71 monomers, 8327.546 Da Detail

SAPGGKSRRR RTAFTSEQLL ELEKEFHCKK YLSLTERSQI AHALKLSEVQ VKIWFQNRRA KWKRIKAGNV S

2. DNA 1 (polymer, Thiol state: not present), 14 monomers, 4342.775 Da Detail

CGACTAATTA GTCG

3. DNA 2 (polymer, Thiol state: not present), 14 monomers, 4342.775 Da Detail

CGACTAATTA GTCG

Total weight

17013.096 Da

Max. entity weight

8327.546 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 69.7 %, Completeness: 63.6 %, Completeness (bb): 54.0 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	63.6 % (737 of 1159)	55.0 % (409 of 744)	75.1 % (253 of 337)	96.2 % (75 of 78)
Backbone	54.0 % (335 of 620)	38.5 % (131 of 340)	65.2 % (137 of 210)	95.7 % (67 of 70)
Sidechain	76.9 % (467 of 607)	68.8 % (278 of 404)	92.8 % (181 of 195)	100.0 % (8 of 8)
Aromatic	50.8 % (64 of 126)	35.2 % (32 of 91)	90.9 % (30 of 33)	100.0 % (2 of 2)
Methyl	84.6 % (66 of 78)	74.4 % (32 of 43)	97.1 % (34 of 35)

1. Gbx1

SAPGGKSRRR RTAFTSEQLL ELEKEFHCKK YLSLTERSQI AHALKLSEVQ VKIWFQNRRA KWKRIKAGNV S

2. DNA 1

CGACTAATTA GTCG

3. DNA 2

CGACTAATTA GTCG

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details The DNA sequence used is double stranded CGACTAATTAGTCG

#	Name	Isotope labeling	Concentration
1	Gbx1	[U-98% 13C; U-98% 15N]	0.8 mM
2	sodium chloride	natural abundance	50 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium azide	natural abundance	5 mM
5	DNA_1	natural abundance	0.8 mM
6	DNA_2	natural abundance	0.8 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

LACS Plot; CA

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

Referencing offset: 2.2 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 2.2 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.07 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2ME0, Strand ID: A Detail

Release date

2016-10-19

Citation

Dynamic Local Polymorphisms in the Gbx1 Homeodomain Induced by DNA Binding
Proudfoot, A.K., Geralt, M., Elsliger, M., Wilson, I.A., Wuthrich, K., Serrano, P.
Structure (2016), 24, 1372-1379, PubMed 27396829 , DOI 10.1016/j.str.2016.05.013 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 18944 released on 2016-10-19
    Title NMR Structure of the homeodomain transcription factor Gbx1 from Homo sapiens
  BMRB: 25849 released on 2015-10-25
    Title NMR Structure of the homeodomain transcription factor Gbx1[E17R,R52E} from Homo sapiens

Related entities 1. Gbx1, : 1 : 2 : 2 : 2 : 270 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC