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BMRB: 34057

5M8I

Solution structure of CUG-BP2 RRM3 in complex with 5'-UUUAA-3' RNA

Authors

Diarra dit Konte, N., Damberger, F.F., Allain, F.H.T.

Assembly

CUGBP Elav-like family member 2/RNA Complex

Entity

1. CUGBP Elav-like family member 2 (polymer), 114 monomers, 12822.51 Da Detail

MGSSHHHHHH SSGLVPRGSH MQKEGPEGAN LFIYHLPQEF GDQDILQMFM PFGNVISAKV FIDKQTNLSK CFGFVSYDNP VSAQAAIQAM NGFQIGMKRL KVQLKRSKND SKPW

2. RNA (5'-R(*UP*UP*UP*AP*A)-3') (polymer, Thiol state: not present), 5 monomers, 1594.924 Da Detail

UUUAA

Total weight

14417.434 Da

Max. entity weight

12822.51 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, coupling_constants

Chem. Shift Complete1

Sequence coverage: 85.7 %, Completeness: 76.1 %, Completeness (bb): 69.9 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	76.1 % (1097 of 1441)	83.8 % (634 of 757)	63.0 % (351 of 557)	88.2 % (112 of 127)
Backbone	69.9 % (508 of 727)	78.6 % (206 of 262)	57.7 % (206 of 357)	88.9 % (96 of 108)
Sidechain	83.3 % (681 of 818)	86.5 % (428 of 495)	78.0 % (237 of 304)	84.2 % (16 of 19)
Aromatic	53.0 % (88 of 166)	65.1 % (54 of 83)	41.8 % (33 of 79)	25.0 % (1 of 4)
Methyl	97.8 % (88 of 90)	100.0 % (45 of 45)	95.6 % (43 of 45)

1. CUGBP Elav-like family member 2

MGSSHHHHHH SSGLVPRGSH MQKEGPEGAN LFIYHLPQEF GDQDILQMFM PFGNVISAKV FIDKQTNLSK CFGFVSYDNP VSAQAAIQAM NGFQIGMKRL KVQLKRSKND SKPW

2. RNA (5'-R(*UP*UP*UP*AP*A)-3')

UUUAA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8, Details 0.6 mM [U-99% 13C; U-99% 15N] CUG-BP2 third RNA Recognition Motif, 1.8 mM unlabeled 5'-UUUAA-3' RNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	5'-UUUAA-3' RNA	non-labeled	1.8 mM
2	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.6 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8, Details 0.8 mM [U-99% 13C; U-99% 15N] CUG-BP2 third RNA Recognition Motif, 0.8 mM non-labeled 5'-UUUAA-3' RNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
5	5'-UUUAA-3' RNA	non-labeled	0.8 mM
6	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.8 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8, Details 0.8 mM [U-99% 15N] CUG-BP2 third RNA Recognition Motif, 0.8 mM non-labeled 5'-UUUAA-3' RNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
9	5'-UUUAA-3' RNA	non-labeled	0.8 mM
10	CUG-BP2 third RNA Recognition Motif	[U-99% 15N]	0.8 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

Chem. Shift Complete2

Sequence coverage: 16.0 %, Completeness: 44.1 %, Completeness (bb): 42.1 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	44.1 % (1271 of 2882)	49.0 % (742 of 1514)	36.2 % (403 of 1114)	49.6 % (126 of 254)
Backbone	42.1 % (612 of 1454)	50.0 % (262 of 524)	33.8 % (241 of 714)	50.5 % (109 of 216)
Sidechain	46.3 % (758 of 1636)	48.5 % (480 of 990)	42.9 % (261 of 608)	44.7 % (17 of 38)
Aromatic	29.5 % (98 of 332)	38.6 % (64 of 166)	20.9 % (33 of 158)	12.5 % (1 of 8)
Methyl	62.2 % (112 of 180)	63.3 % (57 of 90)	61.1 % (55 of 90)

1. CUGBP Elav-like family member 2

MGSSHHHHHH SSGLVPRGSH MQKEGPEGAN LFIYHLPQEF GDQDILQMFM PFGNVISAKV FIDKQTNLSK CFGFVSYDNP VSAQAAIQAM NGFQIGMKRL KVQLKRSKND SKPW

2. RNA (5'-R(*UP*UP*UP*AP*A)-3')

UUUAA

Show sample condition

Sample #1

#	Name	Isotope labeling	Concentration
1	5'-UUUAA-3' RNA	non-labeled	1.8 mM
2	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.6 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

Sample #2

#	Name	Isotope labeling	Concentration
5	5'-UUUAA-3' RNA	non-labeled	0.8 mM
6	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.8 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

Sample #3

#	Name	Isotope labeling	Concentration
9	5'-UUUAA-3' RNA	non-labeled	0.8 mM
10	CUG-BP2 third RNA Recognition Motif	[U-99% 15N]	0.8 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

LACS Plot; CA

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

Referencing offset: -0.14 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.14 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.0 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5M8I, Strand ID: A Detail

Coupling constant

105 J values in 2 lists
Field strength (¹H) 750 MHz, Pressure 1 atm, Temperature 298 K, pH 5.8 Detail

Release date

2016-11-21

Citation

Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination
Diarra dit Konte, N., Krepl, M., Damberger, F.F., Ripin, N., Duss, O.F., Sponer, J., Allain, F.H.
Nat. Commun. (2017), 8, 654-654, PubMed 28935965 , DOI 10.1038/s41467-017-00631-3 , Abstract

Related entities 1. CUGBP Elav-like family member 2, : 1 : 131 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8, Details 0.6 mM [U-99% 13C; U-99% 15N] CUG-BP2 third RNA Recognition Motif, 1.8 mM unlabeled 5'-UUUAA-3' RNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	5'-UUUAA-3' RNA	non-labeled	1.8 mM
2	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.6 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	5'-UUUAA-3' RNA	non-labeled	1.8 mM
2	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.6 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	5'-UUUAA-3' RNA	non-labeled	1.8 mM
2	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.6 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

4 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	5'-UUUAA-3' RNA	non-labeled	1.8 mM
2	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.6 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

5 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	5'-UUUAA-3' RNA	non-labeled	1.8 mM
2	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.6 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

6 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	5'-UUUAA-3' RNA	non-labeled	1.8 mM
2	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.6 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

7 2D 1H-15N HSQC long range

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	5'-UUUAA-3' RNA	non-labeled	1.8 mM
2	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.6 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

8 3D HNHA

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	5'-UUUAA-3' RNA	non-labeled	1.8 mM
2	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.6 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %

9 2D 1H-1H TOCSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8, Details 0.8 mM [U-99% 13C; U-99% 15N] CUG-BP2 third RNA Recognition Motif, 0.8 mM non-labeled 5'-UUUAA-3' RNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
5	5'-UUUAA-3' RNA	non-labeled	0.8 mM
6	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.8 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

10 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
5	5'-UUUAA-3' RNA	non-labeled	0.8 mM
6	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.8 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

11 2D F2 13C-filtered 1H-1H NOESY

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
5	5'-UUUAA-3' RNA	non-labeled	0.8 mM
6	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.8 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

12 natural abundance 2D 13C-1H HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.8, Details 0.8 mM [U-99% 15N] CUG-BP2 third RNA Recognition Motif, 0.8 mM non-labeled 5'-UUUAA-3' RNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
9	5'-UUUAA-3' RNA	non-labeled	0.8 mM
10	CUG-BP2 third RNA Recognition Motif	[U-99% 15N]	0.8 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

13 3D F1 13C-filtered 1H-1H NOESY 13C-1H HSQC aliphatic

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
5	5'-UUUAA-3' RNA	non-labeled	0.8 mM
6	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.8 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

14 3D F1 13C-filtered 1H-1H NOESY 13C-1H HSQC aromatic

Instrument

Bruker AvanceIII - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
5	5'-UUUAA-3' RNA	non-labeled	0.8 mM
6	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.8 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

15 2D spin-echo difference constant time HN(CO)CG

Instrument

Bruker AvanceIII - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
5	5'-UUUAA-3' RNA	non-labeled	0.8 mM
6	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.8 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

16 2D spin-echo difference constant time 1H-15N HSQC

Instrument

Bruker AvanceIII - 750 MHz

Sample

#	Name	Isotope labeling	Concentration
5	5'-UUUAA-3' RNA	non-labeled	0.8 mM
6	CUG-BP2 third RNA Recognition Motif	[U-99% 13C; U-99% 15N]	0.8 mM
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

nullKeywords RNA, RNA binding protein, RNA recognition motif

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Found 1 Document (0.962 seconds)

BMRB: 34057

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. CUGBP Elav-like family member 2, : 1 : 131 entities Detail

Experiments performed 16 experiments Detail

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