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BMRB: 17835

2LH9

NOT AVAILABLE

Authors

Cui, G., Botuyan, M., Mer, G.

Assembly

TDRD7

Entity

1. TDRD7 (polymer, Thiol state: all free), 78 monomers, 8670.009 Da Detail

GHMLEADLVS KMLRAVLQSH KNGIVLPRLQ GEYRSLTGDW IPFKQLGYPT LEAYLRSVPA VVRIEASRSG EIVCYAVA

Formula weight

8670.009 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.9 %, Completeness (bb): 99.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.9 % (898 of 908)	98.5 % (463 of 470)	99.4 % (357 of 359)	98.7 % (78 of 79)
Backbone	99.1 % (456 of 460)	98.1 % (155 of 158)	100.0 % (228 of 228)	98.6 % (73 of 74)
Sidechain	98.8 % (514 of 520)	98.7 % (308 of 312)	99.0 % (201 of 203)	100.0 % (5 of 5)
Aromatic	93.5 % (58 of 62)	93.5 % (29 of 31)	93.3 % (28 of 30)	100.0 % (1 of 1)
Methyl	100.0 % (106 of 106)	100.0 % (53 of 53)	100.0 % (53 of 53)

1. TDRD7

GHMLEADLVS KMLRAVLQSH KNGIVLPRLQ GEYRSLTGDW IPFKQLGYPT LEAYLRSVPA VVRIEASRSG EIVCYAVA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
1	TDRD7	[U-100% 15N]		1.5 mM
2	sodium acetate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.11 ppm, Outliers: 5 Detail

LACS Plot; CB

Referencing offset: 0.11 ppm, Outliers: 5 Detail

LACS Plot; HA

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.17 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LH9, Strand ID: A Detail

Release date

2012-04-29

Citation

(1)H, (15)N and (13)C resonance assignments for the three LOTUS RNA binding domains of Tudor domain-containing protein TDRD7
Cui, G., Botuyan, M., Mer, G.
Biomol. NMR Assign. (2013), 7, 79-83, PubMed 22481467 , DOI 10.1007/s12104-012-9382-1 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 18211 released on 2012-03-19
Title 1H, 15N and 13C resonance assignments for the LOTUS2 and LOTUS3 RNA binding domains of mouse TDRD7

Related entities 1. TDRD7, : 1 : 4 : 46 entities Detail

Interaction partners 1. TDRD7, : 17 interactors Detail

More details for 17 interactors identified by 5 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
1	TDRD7	[U-100% 15N]		1.5 mM
2	sodium acetate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
1	TDRD7	[U-100% 15N]		1.5 mM
2	sodium acetate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

4 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

7 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

8 3D HN(CA)CO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

9 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

10 3D CCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

13 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

14 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.3

#	Name	Isotope labeling	Type	Concentration
5	TDRD7	[U-100% 13C; U-100% 15N]		1.5 mM
6	sodium acetate	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17835_2lh9.nef
Input source #2: Coordindates	2lh9.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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	78	0	0	100.0

Content subtype: combined_17835_2lh9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	908		100.0 (chain: A, length: 78)
1	Distance restraints	AMBER_distance_constraints_3	OK	13608 (1)	noe	100.0 (chain: A, length: 78)
1	Dihedral angle restraints	AMBER_dihedral_2	OK	187 (187)	.	97.4 (chain: A, length: 78)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 467
  - ¹³C chemical shifts: 357
  - ¹⁵N chemical shifts: 84
- 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: AMBER_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 100.0%
- Total number of restraints: 13362
- Weight of restraints: 1.0 (13362)
- Potential type of restraints: square-well-parabolic (13362)
- Range of distance target values: 2.25, 8.27 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: AMBER_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 78, Sequence coverage: 97.4%
- Total number of restraints: 187
- Total number of restraints per polymer type: 187
- Weight of restraints: 1.0 (187)
- Potential type of restraints: square-well-parabolic (187)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Ribonucleoprotein, RNA binding domain, RNA granule component, Tudor domain-containing protein