BMRBj - BMREntryMaster

Found 1 Document (1.107 seconds)

BMRB: 19776

2MKI

Solution structure of tandem RRM domains of cytoplasmic polyadenylation element binding protein 4 (CPEB4) in complex with RNA

Authors

Afroz, T., Skrisovska, L., Belloc, E., Boixet, J.G., Mendez, R., Allain, F.H.-T.

Assembly

CPEB4RRM12 in complex with RNA

Entity

1. CPEB4RRM12 (polymer, Thiol state: all free), 203 monomers, 22797.72 Da Detail

SHQNGERVER YSRKVFVGGL PPDIDEDEIT ASFRRFGPLI VDWPHKAESK SYFPPKGYAF LLFQDESSVQ ALIDACIEED GKLYLCVSSP TIKDKPVQIR PWNLSDSDFV MDGSQPLDPR KTIFVGGVPR PLRAVELAMI MDRLYGGVCY AGIDTDPELK YPKGAGRVAF SNQQSYIAAI SARFVQLQHG EIDKRVEVKP YVL

2. RNA (5'-CUUUA)-3') (polymer, Thiol state: not present), 5 monomers, 1570.900 Da Detail

CUUUA

Total weight

24368.621 Da

Max. entity weight

22797.72 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.7 %, Completeness: 71.5 %, Completeness (bb): 72.0 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	71.5 % (1768 of 2472)	77.0 % (996 of 1294)	60.5 % (589 of 974)	89.7 % (183 of 204)
Backbone	72.0 % (894 of 1241)	85.1 % (370 of 435)	56.7 % (351 of 619)	92.5 % (173 of 187)
Sidechain	72.2 % (1024 of 1419)	72.9 % (626 of 859)	71.5 % (388 of 543)	58.8 % (10 of 17)
Aromatic	64.5 % (151 of 234)	82.1 % (96 of 117)	47.3 % (53 of 112)	40.0 % (2 of 5)
Methyl	90.7 % (194 of 214)	89.7 % (96 of 107)	91.6 % (98 of 107)

1. CPEB4RRM12

2. RNA (5'-CUUUA)-3')

CUUUA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	CPEB4RRM12	[U-100% 13C; U-100% 15N]	0.6 mM
5	5'-CUUUA-3'	natural abundance	0.6 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	CPEB4RRM12	[U-100% 13C; U-100% 15N]	0.4 ~ 0.6 mM
9	RNA (5'-CUUUA)-3')	natural abundance	0.4 ~ 0.6 mM
10	sodium chloride	natural abundance	100 mM
11	DTT	natural abundance	1 mM
12	sodium phosphate	natural abundance	50 mM
13	D2O	natural abundance	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
14	CPEB4RRM12	[U-100% 13C; U-100% 15N; U-80% 2H]	0.4 ~ 0.6 mM
15	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
16	sodium chloride	natural abundance	100 mM
17	DTT	natural abundance	1 mM
18	sodium phosphate	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
21	CPEB4RRM12	[U-100% 15N]	0.4 ~ 0.6 mM
22	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
23	sodium chloride	natural abundance	100 mM
24	DTT	natural abundance	1 mM
25	potassium phosphate	natural abundance	50 mM
26	D2O	natural abundance	100 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
27	CPEB4RRM12	[U-100% 15N]	0.4 ~ 0.6 mM
28	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
29	sodium chloride	natural abundance	100 mM
30	DTT	natural abundance	1 mM
31	potassium phosphate	natural abundance	50 mM
32	H2O	natural abundance	90 %
33	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	water	protons	4.702 ppm	internal	direct	1.0

Referencing offset: 3.29 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	water	protons	4.702 ppm	internal	direct	1.0

Referencing offset: 3.29 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	water	protons	4.702 ppm	internal	direct	1.0

Referencing offset: -0.03 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2014-07-20

Citation

A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins
Afroz, T., Skrisovska, L., Belloc, E.G., Boixet, J.G., Mendez, R., Allain, F.H.-T.
Genes. Dev. (2014), 28, 1498-1514, PubMed 24990967 , DOI 10.1101/gad.241133.114 , Abstract

Related entities 1. CPEB4RRM12, : 1 : 3 : 7 : 124 entities Detail

Experiments performed 21 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
27	CPEB4RRM12	[U-100% 15N]	0.4 ~ 0.6 mM
28	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
29	sodium chloride	natural abundance	100 mM
30	DTT	natural abundance	1 mM
31	potassium phosphate	natural abundance	50 mM
32	H2O	natural abundance	90 %
33	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	CPEB4RRM12	[U-100% 13C; U-100% 15N]	0.4 ~ 0.6 mM
9	RNA (5'-CUUUA)-3')	natural abundance	0.4 ~ 0.6 mM
10	sodium chloride	natural abundance	100 mM
11	DTT	natural abundance	1 mM
12	sodium phosphate	natural abundance	50 mM
13	D2O	natural abundance	100 %

3 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	CPEB4RRM12	[U-100% 13C; U-100% 15N]	0.4 ~ 0.6 mM
9	RNA (5'-CUUUA)-3')	natural abundance	0.4 ~ 0.6 mM
10	sodium chloride	natural abundance	100 mM
11	DTT	natural abundance	1 mM
12	sodium phosphate	natural abundance	50 mM
13	D2O	natural abundance	100 %

4 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	CPEB4RRM12	[U-100% 13C; U-100% 15N]	0.4 ~ 0.6 mM
9	RNA (5'-CUUUA)-3')	natural abundance	0.4 ~ 0.6 mM
10	sodium chloride	natural abundance	100 mM
11	DTT	natural abundance	1 mM
12	sodium phosphate	natural abundance	50 mM
13	D2O	natural abundance	100 %

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
27	CPEB4RRM12	[U-100% 15N]	0.4 ~ 0.6 mM
28	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
29	sodium chloride	natural abundance	100 mM
30	DTT	natural abundance	1 mM
31	potassium phosphate	natural abundance	50 mM
32	H2O	natural abundance	90 %
33	D2O	natural abundance	10 %

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
21	CPEB4RRM12	[U-100% 15N]	0.4 ~ 0.6 mM
22	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
23	sodium chloride	natural abundance	100 mM
24	DTT	natural abundance	1 mM
25	potassium phosphate	natural abundance	50 mM
26	D2O	natural abundance	100 %

7 3D trHNCA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
14	CPEB4RRM12	[U-100% 13C; U-100% 15N; U-80% 2H]	0.4 ~ 0.6 mM
15	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
16	sodium chloride	natural abundance	100 mM
17	DTT	natural abundance	1 mM
18	sodium phosphate	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

8 3D trHN(CO)CA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
14	CPEB4RRM12	[U-100% 13C; U-100% 15N; U-80% 2H]	0.4 ~ 0.6 mM
15	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
16	sodium chloride	natural abundance	100 mM
17	DTT	natural abundance	1 mM
18	sodium phosphate	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

9 3D trCBCA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
14	CPEB4RRM12	[U-100% 13C; U-100% 15N; U-80% 2H]	0.4 ~ 0.6 mM
15	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
16	sodium chloride	natural abundance	100 mM
17	DTT	natural abundance	1 mM
18	sodium phosphate	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

10 3D trHNCACB

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
14	CPEB4RRM12	[U-100% 13C; U-100% 15N; U-80% 2H]	0.4 ~ 0.6 mM
15	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
16	sodium chloride	natural abundance	100 mM
17	DTT	natural abundance	1 mM
18	sodium phosphate	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

11 3D trHNCO

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
14	CPEB4RRM12	[U-100% 13C; U-100% 15N; U-80% 2H]	0.4 ~ 0.6 mM
15	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
16	sodium chloride	natural abundance	100 mM
17	DTT	natural abundance	1 mM
18	sodium phosphate	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

12 3D trHCACO

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
14	CPEB4RRM12	[U-100% 13C; U-100% 15N; U-80% 2H]	0.4 ~ 0.6 mM
15	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
16	sodium chloride	natural abundance	100 mM
17	DTT	natural abundance	1 mM
18	sodium phosphate	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

13 3D HCcH-TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	CPEB4RRM12	[U-100% 13C; U-100% 15N]	0.6 mM
5	5'-CUUUA-3'	natural abundance	0.6 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

14 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
27	CPEB4RRM12	[U-100% 15N]	0.4 ~ 0.6 mM
28	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
29	sodium chloride	natural abundance	100 mM
30	DTT	natural abundance	1 mM
31	potassium phosphate	natural abundance	50 mM
32	H2O	natural abundance	90 %
33	D2O	natural abundance	10 %

15 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
14	CPEB4RRM12	[U-100% 13C; U-100% 15N; U-80% 2H]	0.4 ~ 0.6 mM
15	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
16	sodium chloride	natural abundance	100 mM
17	DTT	natural abundance	1 mM
18	sodium phosphate	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

16 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
14	CPEB4RRM12	[U-100% 13C; U-100% 15N; U-80% 2H]	0.4 ~ 0.6 mM
15	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
16	sodium chloride	natural abundance	100 mM
17	DTT	natural abundance	1 mM
18	sodium phosphate	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

17 3D hCCH TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
14	CPEB4RRM12	[U-100% 13C; U-100% 15N; U-80% 2H]	0.4 ~ 0.6 mM
15	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
16	sodium chloride	natural abundance	100 mM
17	DTT	natural abundance	1 mM
18	sodium phosphate	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

18 2D 1H-15N TROSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
27	CPEB4RRM12	[U-100% 15N]	0.4 ~ 0.6 mM
28	5'-CUUUA-3'	natural abundance	0.4 ~ 0.6 mM
29	sodium chloride	natural abundance	100 mM
30	DTT	natural abundance	1 mM
31	potassium phosphate	natural abundance	50 mM
32	H2O	natural abundance	90 %
33	D2O	natural abundance	10 %

19 2D 13C F1-filtered F2-filtered NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	CPEB4RRM12	[U-100% 13C; U-100% 15N]	0.6 mM
5	5'-CUUUA-3'	natural abundance	0.6 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

20 2D 1H-1H F1-13C-filtered F2-13C-edited NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	CPEB4RRM12	[U-100% 13C; U-100% 15N]	0.6 mM
5	5'-CUUUA-3'	natural abundance	0.6 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

21 3D 13C F1-edited, F3-filtered NOESY HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	1 mM
4	CPEB4RRM12	[U-100% 13C; U-100% 15N]	0.6 mM
5	5'-CUUUA-3'	natural abundance	0.6 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

nullKeywords CPEB4, Cytoplasmic polyadenylation, Protein-RNA Interaction, RNA recognition motif (RRM), Translational regulation

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Found 1 Document (1.107 seconds)

BMRB: 19776

Sample #1

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Sample #5

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. CPEB4RRM12, : 1 : 3 : 7 : 124 entities Detail

Experiments performed 21 experiments Detail

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