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BMRB: 25160

2MTG

NMR structure of the RRM1 of human LARP6

Authors

Martino, L., Atkinson, A.R., Kelly, G., Conte, M.R.

Assembly

RRM1 of human LARP6

Entity

1. RRM1 of human LARP6 (polymer), 116 monomers, 13114.28 Da Detail

NLPSKMLLVY DLYLSPKLWA LATPQKNGRV QEKVMEHLLK LFGTFGVISS VRILKPGREL PPDIRRISSR YSQVGTQECA IVEFEEVEAA IKAHEFMITE SQGKENMKAV LIGMKP

Formula weight

13114.28 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: 80.9 %, Completeness (bb): 91.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.9 % (1137 of 1405)	77.8 % (574 of 738)	83.4 % (458 of 549)	89.0 % (105 of 118)
Backbone	91.3 % (623 of 682)	90.9 % (211 of 232)	90.9 % (310 of 341)	93.6 % (102 of 109)
Sidechain	74.0 % (616 of 832)	71.7 % (363 of 506)	78.9 % (250 of 317)	33.3 % (3 of 9)
Aromatic	88.1 % (74 of 84)	88.1 % (37 of 42)	87.8 % (36 of 41)	100.0 % (1 of 1)
Methyl	85.2 % (121 of 142)	88.7 % (63 of 71)	81.7 % (58 of 71)

1. LARP6 RRM1

NLPSKMLLVY DLYLSPKLWA LATPQKNGRV QEKVMEHLLK LFGTFGVISS VRILKPGREL PPDIRRISSR YSQVGTQECA IVEFEEVEAA IKAHEFMITE SQGKENMKAV LIGMKP

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 RRM1	[U-95% 13C; U-95% 15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.23 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MTG, 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
Martino, L., Pennell, S., Kelly, G., Busi, B., Brown, P., Atkinson, A.R., Salisbury, N.JH., Ooi, Z.H., See, K.W., Smerdon, S.J., Alfano, C., Bui, T., 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. RRM1 of human LARP6, : 1 : 2 : 6 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 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 RRM1	[U-95% 13C; U-95% 15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 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 RRM1	[U-95% 13C; U-95% 15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Varian INOVA - 800 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 RRM1	[U-95% 13C; U-95% 15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D HNCA

Instrument

Varian INOVA - 800 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 RRM1	[U-95% 13C; U-95% 15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Varian INOVA - 800 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 RRM1	[U-95% 13C; U-95% 15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 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 RRM1	[U-95% 13C; U-95% 15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 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 RRM1	[U-95% 13C; U-95% 15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

8 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 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 RRM1	[U-95% 13C; U-95% 15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

9 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 800 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 RRM1	[U-95% 13C; U-95% 15N]		0.5 mM
2	TRIS	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25160_2mtg.nef
Input source #2: Coordindates	2mtg.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

---180-----190-------200-------210-------220-------230-------240-------250-------260-------270------
GNENLPSKMLLVYDLYLSPKLWALATPQKNGRVQEKVMEHLLKLFGTFGVISSVRILKPGRELPPDIRRISSRYSQVGTQECAIVEFEEVEAAIKAHEFM
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GNENLPSKMLLVYDLYLSPKLWALATPQKNGRVQEKVMEHLLKLFGTFGVISSVRILKPGRELPPDIRRISSRYSQVGTQECAIVEFEEVEAAIKAHEFM
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-280-------290-----
ITESQGKENMKAVLIGMKP
|||||||||||||||||||
ITESQGKENMKAVLIGMKP
-------110---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	119	0	0	100.0

Content subtype: combined_25160_2mtg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1124		94.1 (chain: A, length: 119)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1448 (1)	noe	85.7 (chain: A, length: 119)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	70 (1)	hbond	39.5 (chain: A, length: 119)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	192 (192)	.	92.4 (chain: A, length: 119)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	Warning	19 (19)	.	16.0 (chain: A, length: 119)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 94.1%
- Total number of assignments
  - ¹H chemical shifts: 559
  - ¹³C chemical shifts: 461
  - ¹⁵N chemical shifts: 104
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 85.7%
- Total number of restraints: 1411
- Weight of restraints: 1.0 (1411)
- Potential type of restraints: square-well-parabolic (1411)
- Range of distance target values: 2.4, 3.5 (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_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 39.5%
  - Total number of restraints: 70
  - Weight of restraints: 1.0 (70)
  - Potential type of restraints: square-well-parabolic (70)
  - 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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 92.4%
- Total number of restraints: 192
- Total number of restraints per polymer type: 192
- Weight of restraints: 1.0 (192)
- Potential type of restraints: square-well-parabolic (192)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 16.0%
- Total number of restraints: 19
- Potential type of restraints: undefined (19)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords LARP6, RRM, Collagen mRNA, Acheron, LARPs