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BMRB: 18292

2LQ5

NMR structure of the RNA binding motif 39 (RBM39) from Mus musculus

Authors

Serrano, P., Dutta, S.K., Geralt, M., Wuthrich, K.

Assembly

RBM39

Entity

1. RBM39 (polymer, Thiol state: all free), 113 monomers, 12504.10 Da Detail

VQPLATQCFQ LSNMFNPQTE EEVGWDTEIK DDVIEECNKH GGVIHIYVDK NSAQGNVYVK CPSIAAAIAA VNALHGRWFA GKMITAAYVP LPTYHNLFPD SMTATQLLVP SRR

Formula weight

12504.1 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.1 %, Completeness (bb): 98.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.1 % (1233 of 1297)	94.2 % (628 of 667)	95.1 % (484 of 509)	100.0 % (121 of 121)
Backbone	98.0 % (651 of 664)	98.7 % (222 of 225)	97.0 % (323 of 333)	100.0 % (106 of 106)
Sidechain	93.1 % (689 of 740)	91.9 % (406 of 442)	94.7 % (268 of 283)	100.0 % (15 of 15)
Aromatic	85.7 % (96 of 112)	87.5 % (49 of 56)	83.3 % (45 of 54)	100.0 % (2 of 2)
Methyl	97.0 % (130 of 134)	97.0 % (65 of 67)	97.0 % (65 of 67)

1. entity

VQPLATQCFQ LSNMFNPQTE EEVGWDTEIK DDVIEECNKH GGVIHIYVDK NSAQGNVYVK CPSIAAAIAA VNALHGRWFA GKMITAAYVP LPTYHNLFPD SMTATQLLVP SRR

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RBM39	[U-95% 13C; U-95% 15N]		1.2 mM
2	sodium azide	natural abundance		4.5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 2.67 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.67 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.11 ppm, Outliers: 5 Detail

LACS Plot; CO

Referencing offset: 2.87 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LQ5, Strand ID: A Detail

Release date

2012-03-21

Citation

NMR structure of the RNA binding motif 39 (RBM39) from Mus musculus
Serrano, P., Dutta, S.K., Geralt, M., Wuthrich, K.
Not known

Related entities 1. RBM39, : 1 : 9 : 3 : 71 entities Detail

Interaction partners 1. RBM39, : 127 interactors Detail

More details for 127 interactors identified by 26 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RBM39	[U-95% 13C; U-95% 15N]		1.2 mM
2	sodium azide	natural abundance		4.5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RBM39	[U-95% 13C; U-95% 15N]		1.2 mM
2	sodium azide	natural abundance		4.5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RBM39	[U-95% 13C; U-95% 15N]		1.2 mM
2	sodium azide	natural abundance		4.5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RBM39	[U-95% 13C; U-95% 15N]		1.2 mM
2	sodium azide	natural abundance		4.5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 4D APSY HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RBM39	[U-95% 13C; U-95% 15N]		1.2 mM
2	sodium azide	natural abundance		4.5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 5D APSY CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RBM39	[U-95% 13C; U-95% 15N]		1.2 mM
2	sodium azide	natural abundance		4.5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 5D APSY HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RBM39	[U-95% 13C; U-95% 15N]		1.2 mM
2	sodium azide	natural abundance		4.5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RBM39	[U-95% 13C; U-95% 15N]		1.2 mM
2	sodium azide	natural abundance		4.5 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		25 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18292_2lq5.nef
Input source #2: Coordindates	2lq5.cif
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

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
VQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPD

-------110---
SMTATQLLVPSRR
|||||||||||||
SMTATQLLVPSRR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	113	0	0	100.0

Content subtype: combined_18292_2lq5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1218		99.1 (chain: A, length: 113)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2338 (1)	noe	99.1 (chain: A, length: 113)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 622
  - ¹³C chemical shifts: 476
  - ¹⁵N chemical shifts: 120
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 99.1%
- Total number of restraints: 2338
- Weight of restraints: 1.0 (2338)
- Potential type of restraints: upper-bound-parabolic (2338)
- Range of distance target values: 2.4, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords RNA binding domain