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BMRB: 19232

2M88

NMR structure of a two-domain RNA-binding fragment of Nrd1

Authors

Bacikova, V., Pasulka, J., Kubicek, K., Stefl, R.

Assembly

two-domain RNA-binding fragment of Nrd1

Entity

1. two-domain RNA-binding fragment of Nrd1 (polymer), 185 monomers, 20569.00 Da Detail

PDELNVSNNP HYRPKPVSYD STLPPDHIKV YSRTLFIGGV PLNMKEWDLA NVLKPFAEVQ SVILNNSRKH AFVKVYSRHE AENVLQNFNK DGALPLRTRW GVGFGPRDCC DYQHGYSIIP MHRLTDADKK WSVSAQWGGT SGQPLVTGIV FEEPDIIVGE GVSSKAISQK MPTDSGRNGP RSGKP

Formula weight

20569.0 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

torsion angle dynamics, simulated annealing, molecular dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 71.4 %, Completeness: 24.1 %, Completeness (bb): 28.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	24.1 % (519 of 2151)	23.6 % (266 of 1126)	14.6 % (122 of 835)	68.9 % (131 of 190)
Backbone	28.4 % (306 of 1078)	37.8 % (140 of 370)	7.2 % (39 of 539)	75.1 % (127 of 169)
Sidechain	18.0 % (223 of 1242)	16.7 % (126 of 756)	20.0 % (93 of 465)	19.0 % (4 of 21)
Aromatic	8.9 % (16 of 180)	8.9 % (8 of 90)	4.7 % (4 of 86)	100.0 % (4 of 4)
Methyl	63.5 % (113 of 178)	64.0 % (57 of 89)	62.9 % (56 of 89)

1. entity

PDELNVSNNP HYRPKPVSYD STLPPDHIKV YSRTLFIGGV PLNMKEWDLA NVLKPFAEVQ SVILNNSRKH AFVKVYSRHE AENVLQNFNK DGALPLRTRW GVGFGPRDCC DYQHGYSIIP MHRLTDADKK WSVSAQWGGT SGQPLVTGIV FEEPDIIVGE GVSSKAISQK MPTDSGRNGP RSGKP

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		300 mM
4	beta-mercaptoethanol	natural abundance		10 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N; U-80% 2H]		0.4 mM
6	sodium phosphate	natural abundance		50 mM
7	sodium chloride	natural abundance		300 mM
8	beta-mercaptoethanol	natural abundance		10 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8, Details selectively protonated I, L, V amino acids

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N; U-2H]		0.4 mM
10	sodium phosphate	natural abundance		50 mM
11	sodium chloride	natural abundance		300 mM
12	beta-mercaptoethanol	natural abundance		10 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2M88, Strand ID: A Detail

Release date

2014-05-11

Citation

Structure and semi-sequence-specific RNA binding of Nrd1
Bacikova, V., Pasulka, J., Kubicek, K., Stefl, R.
Nucleic Acids Res. (2014), 42, 8024-8038, PubMed 24860164 , DOI 10.1093/nar/gku446 , Abstract

Related entities 1. two-domain RNA-binding fragment of Nrd1, : 1 : 2 : 6 : 3 entities Detail

Interaction partners 1. two-domain RNA-binding fragment of Nrd1, : 28 interactors Detail

More details for 28 interactors identified by 7 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		300 mM
4	beta-mercaptoethanol	natural abundance		10 mM

2 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		300 mM
4	beta-mercaptoethanol	natural abundance		10 mM

3 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		300 mM
4	beta-mercaptoethanol	natural abundance		10 mM

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		300 mM
4	beta-mercaptoethanol	natural abundance		10 mM

5 3D HN(COCA)CB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		0.4 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		300 mM
4	beta-mercaptoethanol	natural abundance		10 mM

6 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N; U-80% 2H]		0.4 mM
6	sodium phosphate	natural abundance		50 mM
7	sodium chloride	natural abundance		300 mM
8	beta-mercaptoethanol	natural abundance		10 mM

7 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N; U-80% 2H]		0.4 mM
6	sodium phosphate	natural abundance		50 mM
7	sodium chloride	natural abundance		300 mM
8	beta-mercaptoethanol	natural abundance		10 mM

8 3D HCACO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N; U-80% 2H]		0.4 mM
6	sodium phosphate	natural abundance		50 mM
7	sodium chloride	natural abundance		300 mM
8	beta-mercaptoethanol	natural abundance		10 mM

9 4D HCCH methyl NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8, Details selectively protonated I, L, V amino acids

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N; U-2H]		0.4 mM
10	sodium phosphate	natural abundance		50 mM
11	sodium chloride	natural abundance		300 mM
12	beta-mercaptoethanol	natural abundance		10 mM

10 3D HCCCONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8, Details selectively protonated I, L, V amino acids

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N; U-2H]		0.4 mM
10	sodium phosphate	natural abundance		50 mM
11	sodium chloride	natural abundance		300 mM
12	beta-mercaptoethanol	natural abundance		10 mM

11 3D CCH TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 8, Details selectively protonated I, L, V amino acids

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-13C; U-15N; U-2H]		0.4 mM
10	sodium phosphate	natural abundance		50 mM
11	sodium chloride	natural abundance		300 mM
12	beta-mercaptoethanol	natural abundance		10 mM

nullKeywords NMR spectroscopy, Nrd1 complex, RNA binding, RNA processing and degradation, RRM structure