BMRBj - BMREntryMaster

Found 1 Document (0.848 seconds)

BMRB: 34428

6SO9

Mouse RBM20 RRM domain in complex with AUCUUA RNA

Authors

Mackereth, C.D., Upadhyay, S.K.

Assembly

RNA-binding protein 20/RNA Complex

Entity

1. RNA-binding protein 20/RNA Complex, entity 1 (polymer, Thiol state: not present), 6 monomers, 1820.126 Da Detail

XUCUUA

2. RNA-binding protein 20/RNA Complex, entity 2 (polymer, Thiol state: all free), 112 monomers, 12554.45 Da Detail

GAMAQRKGAG RVVHICNLPE GSCTENDVIN LGLPFGKVTN YILMKSTNQA FLEMAYTEAA QAMVQYYQEK PAIINGEKLL IRMSTRYKEL QLKKPGKNVA AIIQDIHSQR ER

Total weight

14374.576 Da

Max. entity weight

12554.45 Da

Source organism

synthetic construct , Mus musculus

Exptl. method

solution NMR

Refine. method

simulated annealingsimulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.3 %, Completeness: 93.3 %, Completeness (bb): 95.1 % Detail

Polymer type: polyribonucleotide polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.3 % (1313 of 1408)	94.2 % (698 of 741)	91.1 % (493 of 541)	96.8 % (122 of 126)
Backbone	95.1 % (684 of 719)	96.5 % (249 of 258)	92.9 % (328 of 353)	99.1 % (107 of 108)
Sidechain	92.3 % (732 of 793)	93.0 % (449 of 483)	91.8 % (268 of 292)	83.3 % (15 of 18)
Aromatic	83.0 % (78 of 94)	97.9 % (46 of 47)	72.7 % (32 of 44)	0.0 % (0 of 3)
Methyl	97.7 % (125 of 128)	96.9 % (62 of 64)	98.4 % (63 of 64)

1. entity 1

XUCUUA

2. entity 2

GAMAQRKGAG RVVHICNLPE GSCTENDVIN LGLPFGKVTN YILMKSTNQA FLEMAYTEAA QAMVQYYQEK PAIINGEKLL IRMSTRYKEL QLKKPGKNVA AIIQDIHSQR ER

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 400 uM [U-99% 13C; U-99% 15N] Mouse RBM20 RRM domain, 480 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	400 uM
2	AUCUUA	natural abundance	480 uM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 400 uM [U-99% 15N] Mouse RBM20 RRM domain, 480 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	Mouse RBM20 RRM domain	[U-99% 15N]	400 uM
6	AUCUUA	natural abundance	480 uM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 500 uM [U-99% 13C; U-99% 15N] Mouse RBM20 RRM domain, 600 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	500 uM
10	AUCUUA	natural abundance	600 uM
11	sodium phosphate	natural abundance	20 mM
12	sodium chloride	natural abundance	50 mM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 300 uM [U-99% 2H; U-99% 15N] Mouse RBM20 RRM domain, 290 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
13	Mouse RBM20 RRM domain	[U-99% 2H; U-99% 15N]	300 uM
14	AUCUUA	natural abundance	290 uM
15	sodium phosphate	natural abundance	20 mM
16	sodium chloride	natural abundance	50 mM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 300 uM [U-99% 13C] Mouse RBM20 RRM domain, 360 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
17	Mouse RBM20 RRM domain	[U-99% 13C]	300 uM
18	AUCUUA	natural abundance	360 uM
19	sodium phosphate	natural abundance	20 mM
20	sodium chloride	natural abundance	50 mM

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 450 uM [U-10% 13C; U-99% 15N] Mouse RBM20 RRM domain, 560 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
21	Mouse RBM20 RRM domain	[U-10% 13C; U-99% 15N]	450 uM
22	AUCUUA	natural abundance	560 uM
23	sodium phosphate	natural abundance	20 mM
24	sodium chloride	natural abundance	50 mM

Sample #7

#	Name	Isotope labeling	Concentration
25	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	500 uM
26	AUCUUA	natural abundance	600 uM
27	sodium phosphate	natural abundance	20 mM
28	sodium chloride	natural abundance	50 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
¹H	water	protons	4.772 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
¹H	water	protons	4.772 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
¹H	water	protons	4.772 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	internal	indirect	0.2514495
¹H	water	protons	4.772 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: 0.19 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 25 models in PDB: 6SO9, Strand ID: A Detail

Release date

2019-10-24

Citation

Structural basis of UCUU RNA motif recognition by splicing factor RBM20
Upadhyay, S.K., Mackereth, C.D.
Nucleic Acids Res. (2020), 48, 4538-4550, PubMed 32187365 , DOI 10.1093/nar/gkaa168 , Abstract

Related entities 2. RNA-binding protein 20/RNA Complex, entity 2, : 1 : 1 : 2 : 41 entities Detail

Interaction partners 2. RNA-binding protein 20/RNA Complex, entity 2, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Neo - 700 MHz TXI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 400 uM [U-99% 13C; U-99% 15N] Mouse RBM20 RRM domain, 480 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	400 uM
2	AUCUUA	natural abundance	480 uM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

2 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 800 MHz cryoprobe TCI

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 300 uM [U-99% 13C] Mouse RBM20 RRM domain, 360 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
17	Mouse RBM20 RRM domain	[U-99% 13C]	300 uM
18	AUCUUA	natural abundance	360 uM
19	sodium phosphate	natural abundance	20 mM
20	sodium chloride	natural abundance	50 mM

3 3D HNCO

Instrument

Bruker Neo - 700 MHz TXI

Sample

#	Name	Isotope labeling	Concentration
1	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	400 uM
2	AUCUUA	natural abundance	480 uM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

4 3D HN(CA)CO

Instrument

Bruker Neo - 700 MHz TXI

Sample

#	Name	Isotope labeling	Concentration
1	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	400 uM
2	AUCUUA	natural abundance	480 uM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

5 3D HNCA

Instrument

Bruker Neo - 700 MHz TXI

Sample

#	Name	Isotope labeling	Concentration
1	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	400 uM
2	AUCUUA	natural abundance	480 uM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

6 3D CBCA(CO)NH

Instrument

Bruker Neo - 700 MHz TXI

Sample

#	Name	Isotope labeling	Concentration
1	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	400 uM
2	AUCUUA	natural abundance	480 uM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

7 3D HNHA

Instrument

Bruker Neo - 700 MHz TXI

Sample

#	Name	Isotope labeling	Concentration
1	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	400 uM
2	AUCUUA	natural abundance	480 uM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

8 3D HCCH-TOCSY

Instrument

Bruker Neo - 700 MHz TXI

Sample

#	Name	Isotope labeling	Concentration
1	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	400 uM
2	AUCUUA	natural abundance	480 uM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

9 3D HCCH-TOCSY

Instrument

Bruker Neo - 700 MHz TXI

Sample

#	Name	Isotope labeling	Concentration
1	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	400 uM
2	AUCUUA	natural abundance	480 uM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

10 2D 1H-13C HSQC CT

Instrument

Bruker Neo - 700 MHz TXI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 450 uM [U-10% 13C; U-99% 15N] Mouse RBM20 RRM domain, 560 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
21	Mouse RBM20 RRM domain	[U-10% 13C; U-99% 15N]	450 uM
22	AUCUUA	natural abundance	560 uM
23	sodium phosphate	natural abundance	20 mM
24	sodium chloride	natural abundance	50 mM

11 3D 1H-15N NOESY

Instrument

Bruker Neo - 700 MHz TXI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 400 uM [U-99% 15N] Mouse RBM20 RRM domain, 480 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	Mouse RBM20 RRM domain	[U-99% 15N]	400 uM
6	AUCUUA	natural abundance	480 uM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM

12 3D 1H-13C NOESY

Instrument

Bruker AVANCE III - 800 MHz cryoprobe TCI

Sample

#	Name	Isotope labeling	Concentration
17	Mouse RBM20 RRM domain	[U-99% 13C]	300 uM
18	AUCUUA	natural abundance	360 uM
19	sodium phosphate	natural abundance	20 mM
20	sodium chloride	natural abundance	50 mM

13 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE III - 800 MHz cryoprobe TCI

Sample

#	Name	Isotope labeling	Concentration
17	Mouse RBM20 RRM domain	[U-99% 13C]	300 uM
18	AUCUUA	natural abundance	360 uM
19	sodium phosphate	natural abundance	20 mM
20	sodium chloride	natural abundance	50 mM

14 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 800 MHz cryoprobe TCI

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 300 uM [U-99% 2H; U-99% 15N] Mouse RBM20 RRM domain, 290 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 100% D2O

#	Name	Isotope labeling	Concentration
13	Mouse RBM20 RRM domain	[U-99% 2H; U-99% 15N]	300 uM
14	AUCUUA	natural abundance	290 uM
15	sodium phosphate	natural abundance	20 mM
16	sodium chloride	natural abundance	50 mM

15 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 800 MHz cryoprobe TCI

Sample

#	Name	Isotope labeling	Concentration
13	Mouse RBM20 RRM domain	[U-99% 2H; U-99% 15N]	300 uM
14	AUCUUA	natural abundance	290 uM
15	sodium phosphate	natural abundance	20 mM
16	sodium chloride	natural abundance	50 mM

16 2D x2-filtered 1H-1H NOESY

Instrument

Bruker Neo - 700 MHz TXI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.5, Details 500 uM [U-99% 13C; U-99% 15N] Mouse RBM20 RRM domain, 600 uM AUCUUA, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
25	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	500 uM
26	AUCUUA	natural abundance	600 uM
27	sodium phosphate	natural abundance	20 mM
28	sodium chloride	natural abundance	50 mM

17 2D 1H-13C HSQC

Instrument

Bruker Neo - 700 MHz TXI

Sample

#	Name	Isotope labeling	Concentration
13	Mouse RBM20 RRM domain	[U-99% 2H; U-99% 15N]	300 uM
14	AUCUUA	natural abundance	290 uM
15	sodium phosphate	natural abundance	20 mM
16	sodium chloride	natural abundance	50 mM

18 2D x2-filtered 1H-1H NOESY

Instrument

Bruker AVANCE III - 800 MHz cryoprobe TCI

Sample

#	Name	Isotope labeling	Concentration
17	Mouse RBM20 RRM domain	[U-99% 13C]	300 uM
18	AUCUUA	natural abundance	360 uM
19	sodium phosphate	natural abundance	20 mM
20	sodium chloride	natural abundance	50 mM

19 3D (H)C(CO)NH-TOCSY

Instrument

Bruker Neo - 700 MHz TXI

Sample

#	Name	Isotope labeling	Concentration
1	Mouse RBM20 RRM domain	[U-99% 13C; U-99% 15N]	400 uM
2	AUCUUA	natural abundance	480 uM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM

20 2D 1H-1H NOESY

Instrument

Bruker Neo - 700 MHz TXI

Sample

#	Name	Isotope labeling	Concentration
21	Mouse RBM20 RRM domain	[U-10% 13C; U-99% 15N]	450 uM
22	AUCUUA	natural abundance	560 uM
23	sodium phosphate	natural abundance	20 mM
24	sodium chloride	natural abundance	50 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34428_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
1	1	ADN	ADENOSINE	Assigned chemical shifts

Content subtype: bmr34428_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1478		100.0 (chain: 1, length: 6), 99.1 (chain: 2, length: 112)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 6, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 112, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 854
  - ¹³C chemical shifts: 501
  - ¹⁵N chemical shifts: 123
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 2

Comp_index_ID	Comp_ID
1	ADN

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	C	HO2'	5.77
4	U	HO2'	5.78
5	U	HO2'	5.777

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	42	93.3
¹³C chemical shifts	35	10	28.6
¹⁵N chemical shifts	3	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	30	100.0
¹³C chemical shifts	25	8	32.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	12	80.0
¹³C chemical shifts	10	2	20.0
¹⁵N chemical shifts	3	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	2	100.0
¹³C chemical shifts	2	1	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	696	663	95.3
¹³C chemical shifts	506	485	95.8
¹⁵N chemical shifts	129	123	95.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	228	225	98.7
¹³C chemical shifts	224	219	97.8
¹⁵N chemical shifts	108	107	99.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	468	438	93.6
¹³C chemical shifts	282	266	94.3
¹⁵N chemical shifts	21	16	76.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	69	100.0
¹³C chemical shifts	69	69	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	34	100.0
¹³C chemical shifts	34	30	88.2

Keywords Alternative splicing, RNA BINDING PROTEIN

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Found 1 Document (0.848 seconds)

BMRB: 34428

Sample #1

Sample #2

Sample #3

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Sample #7

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 2. RNA-binding protein 20/RNA Complex, entity 2, : 1 : 1 : 2 : 41 entities Detail

Interaction partners 2. RNA-binding protein 20/RNA Complex, entity 2, : 2 interactors Detail

Experiments performed 20 experiments Detail

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Chemical shift validation 4 contents Detail