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BMRB: 34643

7VPX

Solution structure of the human SF3A1 ubiquitin-like domain

Authors

de Vries, T., Campagne, S., Allain, F.H.T.

Assembly

Isoform 2 of Splicing factor 3A subunit 1

Entity

1. Isoform 2 of Splicing factor 3A subunit 1 (polymer, Thiol state: not present), 93 monomers, 10223.80 Da Detail

GGSPVSIKVQ VPNMQDKTEW KLNGQVLVFT LPLTDQVSVI KVKIHEATGM PAGKQKLQYE GIFIKDSNSL AYYNMANGAV IHLALKERGG RKK

Formula weight

10223.8 Da

Source organism

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.6 %, Completeness (bb): 98.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.6 % (1081 of 1108)	97.9 % (567 of 579)	97.2 % (414 of 426)	97.1 % (100 of 103)
Backbone	98.0 % (539 of 550)	98.4 % (188 of 191)	97.4 % (263 of 270)	98.9 % (88 of 89)
Sidechain	97.5 % (626 of 642)	97.7 % (379 of 388)	97.9 % (235 of 240)	85.7 % (12 of 14)
Aromatic	95.3 % (61 of 64)	96.9 % (31 of 32)	93.5 % (29 of 31)	100.0 % (1 of 1)
Methyl	100.0 % (112 of 112)	100.0 % (56 of 56)	100.0 % (56 of 56)

1. entity 1

GGSPVSIKVQ VPNMQDKTEW KLNGQVLVFT LPLTDQVSVI KVKIHEATGM PAGKQKLQYE GIFIKDSNSL AYYNMANGAV IHLALKERGG RKK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 2.0 mM [U-13C; U-15N] SF3A1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	SF3A1	[U-13C; U-15N]		2.0 (±0.1) mM
2	Sodium phosphate	natural abundance		10 mM
3	NaCl	natural abundance		50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 1.1 mM [U-100% 15N] SF3A1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	SF3A1	[U-100% 15N]		1.1 (±0.1) mM
5	Sodium phosphate	natural abundance		10 mM
6	NaCl	natural abundance		50 mM

Release date

2021-07-06

Citation

Sequence-specific RNA recognition by an RGG motif connects U1 and U2 snRNP for spliceosome assembly
de Vries, T., Martelly, W., Campagne, S., Sabath, K., Sarnowski, C.P., Wong, J., Leitner, A., Jonas, S., Sharma, S., Allain, F.
Proc. Natl. Acad. Sci. U. S. A. (2022), 119, e2114092119-e2114092119, PubMed 35101980 , DOI 10.1073/pnas.2114092119 , Abstract

Related entities 1. Isoform 2 of Splicing factor 3A subunit 1, : 1 : 2 : 17 : 19 entities Detail

Interaction partners 1. Isoform 2 of Splicing factor 3A subunit 1, : 62 interactors Detail

More details for 62 interactors identified by 26 citations

Experiments performed 9 experiments Detail

1 3D HNCACB

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 2.0 mM [U-13C; U-15N] SF3A1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	SF3A1	[U-13C; U-15N]		2.0 (±0.1) mM
2	Sodium phosphate	natural abundance		10 mM
3	NaCl	natural abundance		50 mM

2 3D CBCA(CO)NH

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 2.0 mM [U-13C; U-15N] SF3A1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	SF3A1	[U-13C; U-15N]		2.0 (±0.1) mM
2	Sodium phosphate	natural abundance		10 mM
3	NaCl	natural abundance		50 mM

3 3D HNCO

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 2.0 mM [U-13C; U-15N] SF3A1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	SF3A1	[U-13C; U-15N]		2.0 (±0.1) mM
2	Sodium phosphate	natural abundance		10 mM
3	NaCl	natural abundance		50 mM

4 3D H(CCO)NH

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 2.0 mM [U-13C; U-15N] SF3A1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	SF3A1	[U-13C; U-15N]		2.0 (±0.1) mM
2	Sodium phosphate	natural abundance		10 mM
3	NaCl	natural abundance		50 mM

5 3D H(CCO)NH

Instrument

Bruker AVANCE NEO - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 2.0 mM [U-13C; U-15N] SF3A1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	SF3A1	[U-13C; U-15N]		2.0 (±0.1) mM
2	Sodium phosphate	natural abundance		10 mM
3	NaCl	natural abundance		50 mM

6 3D 15N-1H HSQC NOESY

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 2.0 mM [U-13C; U-15N] SF3A1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	SF3A1	[U-13C; U-15N]		2.0 (±0.1) mM
2	Sodium phosphate	natural abundance		10 mM
3	NaCl	natural abundance		50 mM

7 3D 13Cali-1H HSQC NOESY

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 2.0 mM [U-13C; U-15N] SF3A1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	SF3A1	[U-13C; U-15N]		2.0 (±0.1) mM
2	Sodium phosphate	natural abundance		10 mM
3	NaCl	natural abundance		50 mM

8 3D 13Caro-1H HSQC NOESY

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 2.0 mM [U-13C; U-15N] SF3A1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	SF3A1	[U-13C; U-15N]		2.0 (±0.1) mM
2	Sodium phosphate	natural abundance		10 mM
3	NaCl	natural abundance		50 mM

9 {1H}-15N heteronuclear NOE

Instrument

Bruker AVIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.0, Details 1.1 mM [U-100% 15N] SF3A1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	SF3A1	[U-100% 15N]		1.1 (±0.1) mM
5	Sodium phosphate	natural abundance		10 mM
6	NaCl	natural abundance		50 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34643_3.str
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

Content subtype: bmr34643_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1192		98.9 (chain: 1, length: 93)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 93, Sequence coverage: 98.9%
- Total number of assignments
  - ¹H chemical shifts: 684
  - ¹³C chemical shifts: 409
  - ¹⁵N chemical shifts: 99
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Keywords SF3A, SPLICING, Spliceosome, U2 snRNP, ubiqutin-like domain