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Found 1 Document (0.799 seconds)

BMRB: 19607

2MGX

The C-terminal domain of SRA1p has a fold more similar to PRP18 than to an RRM and does not directly bind to the SRA1 RNA STR7 region.

Authors

Bilinovich, S.M., Davis, C.M., Morris, D.L., Ray, L.A., Prokop, J.W., Buchan, G.J., Leeper, T.C.

Assembly

C-terminal domain of SRA1p

Entity

1. C-terminal domain of SRA1p (polymer, Thiol state: all free), 131 monomers, 14746.56 Da Detail

GSEAVMEDVL RPLEQALEDC RGHTRKQVCD DISRRLALLQ EQWAGGKLSI PVKKRMALLV QELSSHRWDA ADDIHRSLMV DHVTEVSQWM VGVKRLIAEK RSLFSEEAAN EEKSAATAEK NHTIPGFQQA S

Formula weight

14746.56 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 89.3 %, Completeness (bb): 99.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.3 % (1345 of 1507)	84.5 % (665 of 787)	94.3 % (546 of 579)	95.0 % (134 of 141)
Backbone	99.1 % (773 of 780)	98.9 % (262 of 265)	99.2 % (384 of 387)	99.2 % (127 of 128)
Sidechain	81.7 % (696 of 852)	77.2 % (403 of 522)	90.2 % (286 of 317)	53.8 % (7 of 13)
Aromatic	75.0 % (57 of 76)	73.7 % (28 of 38)	74.3 % (26 of 35)	100.0 % (3 of 3)
Methyl	95.3 % (141 of 148)	95.9 % (71 of 74)	94.6 % (70 of 74)

1. SRA1p C-terminal domain

GSEAVMEDVL RPLEQALEDC RGHTRKQVCD DISRRLALLQ EQWAGGKLSI PVKKRMALLV QELSSHRWDA ADDIHRSLMV DHVTEVSQWM VGVKRLIAEK RSLFSEEAAN EEKSAATAEK NHTIPGFQQA S

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	DTT	natural abundance	2 mM
9	sodium chloride	natural abundance	50 mM
10	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
11	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 15 models in PDB: 2MGX, Strand ID: A Detail

Release date

2014-02-09

Citation

The C-terminal domain of SRA1p has a fold more similar to PRP18 than to an RRM and does not directly bind to the SRA1 RNA STR7 region
Bilinovich, S.M., Davis, C.M., Morris, D.L., Ray, L.A., Prokop, J.W., Buchan, G.J., Leeper, T.C.
J. Mol. Biol. (2014), 426, 1753-1765, PubMed 24486611 , DOI 10.1016/j.jmb.2014.01.007 , Abstract

Related entities 1. C-terminal domain of SRA1p, : 1 : 3 : 5 entities Detail

Interaction partners 1. C-terminal domain of SRA1p, : 11 interactors Detail

More details for 11 interactors identified by 4 citations

Experiments performed 19 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

2 3D HNCO

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

3 3D HNCA

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

4 3D HBHA(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

5 3D HCCH-TOCSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	DTT	natural abundance	2 mM
9	sodium chloride	natural abundance	50 mM
10	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
11	D2O	natural abundance	100 %

6 3D HNCACB

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

7 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	DTT	natural abundance	2 mM
9	sodium chloride	natural abundance	50 mM
10	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
11	D2O	natural abundance	100 %

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

9 2D 1H-1H NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	DTT	natural abundance	2 mM
9	sodium chloride	natural abundance	50 mM
10	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
11	D2O	natural abundance	100 %

10 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	DTT	natural abundance	2 mM
9	sodium chloride	natural abundance	50 mM
10	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
11	D2O	natural abundance	100 %

11 3D HN(COCA)CB

Instrument

Varian INOVA - 750 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

12 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	DTT	natural abundance	2 mM
9	sodium chloride	natural abundance	50 mM
10	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
11	D2O	natural abundance	100 %

13 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

14 3d HNCAintra

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

15 3D HNCACBintra

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

16 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

17 2D HBCBCGCDCDHE

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

18 2D HBCBCGCDHD

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

19 3D HN(CA)CO

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DTT	natural abundance	2 mM
3	sodium chloride	natural abundance	50 mM
4	SRA1p C-terminal domain	[U-98% 13C; U-98% 15N]	0.6 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19607_2mgx.nef
Input source #2: Coordindates	2mgx.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

--110-------120-------130-------140-------150-------160-------170-------180-------190-------200-----
GSEAVMEDVLRPLEQALEDCRGHTRKQVCDDISRRLALLQEQWAGGKLSIPVKKRMALLVQELSSHRWDAADDIHRSLMVDHVTEVSQWMVGVKRLIAEK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSEAVMEDVLRPLEQALEDCRGHTRKQVCDDISRRLALLQEQWAGGKLSIPVKKRMALLVQELSSHRWDAADDIHRSLMVDHVTEVSQWMVGVKRLIAEK
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--210-------220-------230------
RSLFSEEAANEEKSAATAEKNHTIPGFQQAS
|||||||||||||||||||||||||||||||
RSLFSEEAANEEKSAATAEKNHTIPGFQQAS
-------110-------120-------130-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	131	0	0	100.0

Content subtype: combined_19607_2mgx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1311		98.5 (chain: A, length: 131)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1967 (1)	noe	98.5 (chain: A, length: 131)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	56 (1)	hbond	32.8 (chain: A, length: 131)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	177 (177)	.	74.0 (chain: A, length: 131)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 131, Sequence coverage: 98.5%
- Total number of assignments
  - ¹H chemical shifts: 645
  - ¹³C chemical shifts: 536
  - ¹⁵N chemical shifts: 130
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
128	HIS	HD1	6.977
171	HIS	HD1	6.866
180	HIS	HD1	6.692
187	HIS	HD1	6.681

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	787	641	81.4
¹³C chemical shifts	579	536	92.6
¹⁵N chemical shifts	151	130	86.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	265	256	96.6
¹³C chemical shifts	262	258	98.5
¹⁵N chemical shifts	128	123	96.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	522	385	73.8
¹³C chemical shifts	317	278	87.7
¹⁵N chemical shifts	23	7	30.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	72	92.3
¹³C chemical shifts	78	72	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	28	73.7
¹³C chemical shifts	35	26	74.3
¹⁵N chemical shifts	3	3	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 131, Sequence coverage: 98.5%
- Total number of restraints: 1967
- Weight of restraints: 1.0 (1967)
- Potential type of restraints: square-well-parabolic (1967)
- Range of distance target values: 2.1, 5.36 (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: 131, Sequence coverage: 32.8%
  - Total number of restraints: 56
  - Weight of restraints: 1.0 (56)
  - Potential type of restraints: square-well-parabolic (56)
  - Range of distance target values: 2.21, 3.22 (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: 131, Sequence coverage: 74.0%
- Total number of restraints: 177
- Total number of restraints per polymer type: 177
- Weight of restraints: 1.0 (177)
- Potential type of restraints: square-well-parabolic (177)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.799 seconds)

BMRB: 19607

Sample #1

Sample #2

Related entities 1. C-terminal domain of SRA1p, : 1 : 3 : 5 entities Detail

Interaction partners 1. C-terminal domain of SRA1p, : 11 interactors Detail

Experiments performed 19 experiments Detail

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NMR combined restraints 5 contents Detail