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BMRB: 19726

2MJH

Protein-RNA structure

Authors

Daubner, G.M., Allain, F.H.T.

Assembly

GLD-1 KH-QUA2 bound to 5'-CUACUCAUAU-3'

Entity

1. GermLine development Defective 1 (polymer, Thiol state: all free), 142 monomers, 16049.33 Da Detail

LPEPAGDMIS ITEKIYVPKN EYPDYNFVGR ILGPRGMTAK QLEQDTGCKI MVRGKGSMRD KSKESAHRGK ANWEHLEDDL HVLVQCEDTE NRVHIKLQAA LEQVKKLLIP APEGTDELKR KQLMELAIIN GTYRPMKSPN PA

2. 5'-CUACUCAUAU-3' (polymer, Thiol state: not present), 10 monomers, 3145.840 Da Detail

CUACUCAUAU

Total weight

19195.17 Da

Max. entity weight

16049.33 Da

Source organism

Caenorhabditis elegans

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, RDCs

Chem. Shift Complete

Sequence coverage: 99.3 %, Completeness: 76.5 %, Completeness (bb): 74.2 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	76.5 % (1411 of 1845)	87.5 % (858 of 981)	58.0 % (415 of 715)	92.6 % (138 of 149)
Backbone	74.2 % (699 of 942)	91.6 % (315 of 344)	55.2 % (257 of 466)	96.2 % (127 of 132)
Sidechain	79.0 % (818 of 1035)	84.6 % (539 of 637)	70.6 % (269 of 381)	58.8 % (10 of 17)
Aromatic	65.3 % (77 of 118)	91.5 % (54 of 59)	40.7 % (22 of 54)	20.0 % (1 of 5)
Methyl	97.3 % (142 of 146)	97.3 % (71 of 73)	97.3 % (71 of 73)

1. GermLine development Defective 1

LPEPAGDMIS ITEKIYVPKN EYPDYNFVGR ILGPRGMTAK QLEQDTGCKI MVRGKGSMRD KSKESAHRGK ANWEHLEDDL HVLVQCEDTE NRVHIKLQAA LEQVKKLLIP APEGTDELKR KQLMELAIIN GTYRPMKSPN PA

2. 5'-CUACUCAUAU-3'

CUACUCAUAU

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	GLD-1 (aa 195-336)	[U-15N]	0.45 mM
2	5'-CUACUCAUAU-3'	natural abundance	0.45 mM
3	sodium chloride	natural abundance	50 mM
4	sodium phosphate	natural abundance	20 mM
5	DTT	natural abundance	3 mM
6	H2O	natural abundance	90 %
7	D2O	[U-100% 2H]	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	GLD-1 (aa 195-336)	[U-13C; U-15N]	0.45 mM
9	5'-CUACUCAUAU-3'	natural abundance	0.45 mM
10	sodium chloride	natural abundance	50 mM
11	sodium phosphate	natural abundance	20 mM
12	DTT	natural abundance	3 mM
13	H2O	natural abundance	90 %
14	D2O	[U-100% 2H]	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	GLD-1 (aa 195-336)	[U-15N]	0.45 mM
16	5'-CUACUCAUAU-3'	natural abundance	0.45 mM
17	sodium chloride	natural abundance	50 mM
18	sodium phosphate	natural abundance	20 mM
19	DTT	natural abundance	3 mM
20	D2O	[U-100% 2H]	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	GLD-1 (aa 195-336)	[U-13C; U-15N]	0.45 mM
22	5'-CUACUCAUAU-3'	natural abundance	0.45 mM
23	sodium chloride	natural abundance	50 mM
24	sodium phosphate	natural abundance	20 mM
25	DTT	natural abundance	3 mM
26	D2O	[U-100% 2H]	100 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
27	GLD-1 (aa 195-336)	[U-10% 13C; U-100% 15N]	0.45 mM
28	5'-CUACUCAUAU-3'	natural abundance	0.45 mM
29	sodium chloride	natural abundance	50 mM
30	sodium phosphate	natural abundance	20 mM
31	DTT	natural abundance	3 mM
32	H2O	natural abundance	90 %
33	D2O	[U-100% 2H]	10 %

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
34	GLD-1 (aa 195-336)	[U-15N]	0.45 mM
35	5'-CUACUCAUAU-3'	natural abundance	0.45 mM
36	sodium chloride	natural abundance	50 mM
37	sodium phosphate	natural abundance	20 mM
38	DTT	natural abundance	3 mM
39	Pf1 phage	natural abundance	14 mg/mL
40	H2O	natural abundance	90 %
41	D2O	[U-100% 2H]	10 %

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: 2.3 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: 2.3 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: 0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

RDC

36 RDC values in 1 lists
Field strength (¹H) 700 MHz, Pressure 1 atm, Temperature 303 K, pH 6.5 Detail

Release date

2014-05-26

Citation

Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1
Daubner, G.M., Bruemmer, A., Tocchini, C., Gerhardy, S., Ciosk, R., Zavolan, M., Allain, F.H.T.
Nucleic Acids Res. (2014), 42, 8092-8105, PubMed 24838563 , DOI 10.1093/nar/gku445 , Abstract