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BMRB: 16812

2KAE

data-driven model of MED1:DNA complex

Authors

Lowry, J.A., Gamsjaeger, R., Thong, S., Hung, W., Kwan, A.H., Broitman-Maduro, G., Matthews, J.M., Maduro, M., Mackay, J.P.

Assembly

MED1:DNA complex

Entity

1. MED1zf (polymer, Thiol state: free and other bound), 65 monomers, 7693.739 Da Detail

KSFQCSNCSV TETIRWRNIR SKEGIQCNAC FIYQRKYNKT RPVTAVNKYQ KRKLKVQETN GVDSF

2. ZN (non-polymer, Thiol state: not present), 65.409 Da
3. DNA (polymer, Thiol state: not available), 20 monomers, 6195.962 Da Detail

CGGAAAAGTA TACTTTTCCG

Total weight

13955.109 Da

Max. entity weight

7693.739 Da

Source organism

Caenorhabditis elegans

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 75.3 %, Completeness: 49.2 %, Completeness (bb): 58.5 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	49.2 % (492 of 999)	43.6 % (271 of 622)	51.8 % (156 of 301)	85.5 % (65 of 76)
Backbone	58.5 % (309 of 528)	46.1 % (125 of 271)	63.2 % (122 of 193)	96.9 % (62 of 64)
Sidechain	44.9 % (240 of 534)	41.6 % (146 of 351)	53.2 % (91 of 171)	25.0 % (3 of 12)
Aromatic	22.6 % (24 of 106)	17.8 % (13 of 73)	31.3 % (10 of 32)	100.0 % (1 of 1)
Methyl	56.7 % (34 of 60)	54.5 % (18 of 33)	59.3 % (16 of 27)

1. MED1zf

KSFQCSNCSV TETIRWRNIR SKEGIQCNAC FIYQRKYNKT RPVTAVNKYQ KRKLKVQETN GVDSF

3. DNA

CGGAAAAGTA TACTTTTCCG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	40 mM
2	potassium phosphate	natural abundance	20 mM
3	DTT	natural abundance	1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %
6	protein	[U-100% 13C; U-100% 15N	0.5 ~ 1.0 mM

Sample #2

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	sodium chloride	natural abundance	40 mM
8	potassium phosphate	natural abundance	20 mM
9	DTT	natural abundance	1 mM
10	Pf1 phage	natural abundance	6 mg
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %
13	protein	[U-100% 13C; U-100% 15N	0.5 ~ 1.0 mM

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: -0.11 ppm, Outliers: 1 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: -0.11 ppm, Outliers: 1 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: 0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2KAE, Strand ID: A Detail

Release date

2010-04-28

Citation

Structural analysis of MED-1 reveals unexpected diversity in the mechanism of DNA recognition by GATA-type zinc finger domains
Lowry, J.A., Gamsjaeger, R., Thong, S., Hung, W., Kwan, A.H., Broitman-Maduro, G., Matthews, J.M., Maduro, M., Mackay, J.P.
J. Biol. Chem. (2009), 284, 5827-5835, PubMed 19095651 , DOI 10.1074/jbc.M808712200 , Abstract

Related entities 1. MED1zf, : 1 : 1 : 99 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC