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BMRB: 25159

2MTF

Solution structure of the La motif of human LARP6

Authors

Martino, L., Salisbury, N.JH., Atkinson, A.R., Kelly, G., Conte, M.R.

Assembly

LARP6-LaM

Entity

1. LARP6-LaM (polymer, Thiol state: all free), 114 monomers, 13461.10 Da Detail

TASGGENERE DLEQEWKPPD EELIKKLVDQ IEFYFSDENL EKDAFLLKHV RRNKLGYVSV KLLTSFKKVK HLTRDWRTTA HALKYSVVLE LNEDHRKVRR TTPVPLFPNE NLPS

Formula weight

13461.1 Da

Source organism

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 79.1 %, Completeness (bb): 91.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.1 % (1114 of 1409)	77.0 % (571 of 742)	80.3 % (441 of 549)	86.4 % (102 of 118)
Backbone	91.5 % (615 of 672)	93.3 % (210 of 225)	90.3 % (306 of 339)	91.7 % (99 of 108)
Sidechain	71.1 % (603 of 848)	69.8 % (361 of 517)	74.5 % (239 of 321)	30.0 % (3 of 10)
Aromatic	32.5 % (37 of 114)	31.6 % (18 of 57)	30.9 % (17 of 55)	100.0 % (2 of 2)
Methyl	99.2 % (125 of 126)	98.4 % (62 of 63)	100.0 % (63 of 63)

1. entity

TASGGENERE DLEQEWKPPD EELIKKLVDQ IEFYFSDENL EKDAFLLKHV RRNKLGYVSV KLLTSFKKVK HLTRDWRTTA HALKYSVVLE LNEDHRKVRR TTPVPLFPNE NLPS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	LARP6-LaM	[U-95% 13C; U-95% 15N]		0.4 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	L-Arginine	natural abundance		50 mM
6	L-Glutamic acid	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.17 ppm, Outliers: 5 Detail

LACS Plot; CB

Referencing offset: 0.17 ppm, Outliers: 5 Detail

LACS Plot; HA

Referencing offset: 0.1 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: -0.18 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2014-12-21

Citation 1

Synergic interplay of the La motif, RRM1 and the interdomain linker of LARP6 in the recognition of collagen mRNA expands the RNA binding repertoire of the La module
Kelly, G., Busi, B., Martino, L., Pennell, S., Brown, P., Atkinson, A.R., Salisbury, N.JH., Ooi, Z.H., See, K.W., Smerdon, S.J., Alfano, C., Bui, T.TT., Conte, M.R.
Nucleic Acids Res. (2015), 43, 645-660, PubMed 25488812 , DOI 10.1093/nar/gku1287 , Abstract

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Citation 2

1H, 15N and 13C chemical shift assignments of the La motif and RRM1 from human LARP6
Martino, L., Salisbury, N.JH., Brown, P., Kelly, G., Atkinson, A.R., Conte, M.R.
Biomol. NMR Assignments

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Related entities 1. LARP6-LaM, : 1 : 2 : 45 entities Detail

Experiments performed 10 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 7.25

#	Name	Isotope labeling	Type	Concentration
1	LARP6-LaM	[U-95% 13C; U-95% 15N]		0.4 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	L-Arginine	natural abundance		50 mM
6	L-Glutamic acid	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

2 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 7.25

#	Name	Isotope labeling	Type	Concentration
1	LARP6-LaM	[U-95% 13C; U-95% 15N]		0.4 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	L-Arginine	natural abundance		50 mM
6	L-Glutamic acid	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	LARP6-LaM	[U-95% 13C; U-95% 15N]		0.4 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	L-Arginine	natural abundance		50 mM
6	L-Glutamic acid	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

4 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	LARP6-LaM	[U-95% 13C; U-95% 15N]		0.4 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	L-Arginine	natural abundance		50 mM
6	L-Glutamic acid	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 7.25

#	Name	Isotope labeling	Type	Concentration
1	LARP6-LaM	[U-95% 13C; U-95% 15N]		0.4 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	L-Arginine	natural abundance		50 mM
6	L-Glutamic acid	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	LARP6-LaM	[U-95% 13C; U-95% 15N]		0.4 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	L-Arginine	natural abundance		50 mM
6	L-Glutamic acid	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.25

#	Name	Isotope labeling	Type	Concentration
1	LARP6-LaM	[U-95% 13C; U-95% 15N]		0.4 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	L-Arginine	natural abundance		50 mM
6	L-Glutamic acid	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

8 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 7.25

#	Name	Isotope labeling	Type	Concentration
1	LARP6-LaM	[U-95% 13C; U-95% 15N]		0.4 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	L-Arginine	natural abundance		50 mM
6	L-Glutamic acid	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

9 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 7.25

#	Name	Isotope labeling	Type	Concentration
1	LARP6-LaM	[U-95% 13C; U-95% 15N]		0.4 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	L-Arginine	natural abundance		50 mM
6	L-Glutamic acid	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

10 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 7.25

#	Name	Isotope labeling	Type	Concentration
1	LARP6-LaM	[U-95% 13C; U-95% 15N]		0.4 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	L-Arginine	natural abundance		50 mM
6	L-Glutamic acid	natural abundance		50 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25159_2mtf.nef
Input source #2: Coordindates	2mtf.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

-70-------80--------90-------100-------110-------120-------130-------140-------150-------160-------1
GTASGGENEREDLEQEWKPPDEELIKKLVDQIEFYFSDENLEKDAFLLKHVRRNKLGYVSVKLLTSFKKVKHLTRDWRTTAHALKYSVVLELNEDHRKVR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GTASGGENEREDLEQEWKPPDEELIKKLVDQIEFYFSDENLEKDAFLLKHVRRNKLGYVSVKLLTSFKKVKHLTRDWRTTAHALKYSVVLELNEDHRKVR
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

70-------180---
RTTPVPLFPNENLPS
|||||||||||||||
RTTPVPLFPNENLPS
-------110-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	115	0	0	100.0

Content subtype: combined_25159_2mtf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1059		94.8 (chain: A, length: 115)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1183 (1)	noe	79.1 (chain: A, length: 115)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	52 (1)	hbond	32.2 (chain: A, length: 115)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	172 (172)	.	86.1 (chain: A, length: 115)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 94.8%
- Total number of assignments
  - ¹H chemical shifts: 545
  - ¹³C chemical shifts: 416
  - ¹⁵N chemical shifts: 98
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 79.1%
- Total number of restraints: 1176
- Weight of restraints: 1.0 (1176)
- Potential type of restraints: square-well-parabolic (1176)
- Range of distance target values: 1.6, 6.79 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 32.2%
  - Total number of restraints: 52
  - Weight of restraints: 1.0 (52)
  - Potential type of restraints: square-well-parabolic (52)
  - Range of distance target values: 2.1, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 86.1%
- Total number of restraints: 172
- Total number of restraints per polymer type: 172
- Weight of restraints: 1.0 (172)
- Potential type of restraints: square-well-parabolic (172)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords La motif, LARP6, Collagen mRNA, RNA binding protein, LARPs