BMRBj - BMREntryMaster

Found 1 Document (2.681 seconds)

BMRB: 18802

2M09

Structure, phosphorylation and U2AF65 binding of the Nterminal domain of splicing factor 1 during 3 splice site recognition

Authors

Madl, T., Sattler, M., Zhang, Y., Bagdiul, I., Kern, T., Kang, H., Zou, P., Maeusbacher, N., Sieber, S.A., Kraemer, A.

Assembly

SF1N

Entity

1. SF1N (polymer, Thiol state: not present), 121 monomers, 13801.60 Da Detail

GAMEQKTVIP GMPTVIPPGL TREQERAYIV QLQIEDLTRK LRTGDLGIPP NPEDRSPSPE PIYNSEGKRL NTREFRTRKK LEEERHNLIT EMVALNPDFK PPADYKPPAT RVSDKVMIPQ D

Formula weight

13801.6 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.0 %, Completeness (bb): 98.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.0 % (1399 of 1442)	96.6 % (745 of 771)	97.1 % (540 of 556)	99.1 % (114 of 115)
Backbone	98.4 % (683 of 694)	98.7 % (229 of 232)	98.3 % (351 of 357)	98.1 % (103 of 105)
Sidechain	96.1 % (829 of 863)	95.7 % (516 of 539)	96.5 % (303 of 314)	100.0 % (10 of 10)
Aromatic	95.8 % (46 of 48)	100.0 % (24 of 24)	91.7 % (22 of 24)
Methyl	100.0 % (120 of 120)	100.0 % (60 of 60)	100.0 % (60 of 60)

1. entity

GAMEQKTVIP GMPTVIPPGL TREQERAYIV QLQIEDLTRK LRTGDLGIPP NPEDRSPSPE PIYNSEGKRL NTREFRTRKK LEEERHNLIT EMVALNPDFK PPADYKPPAT RVSDKVMIPQ D

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM sodium phosphate (pH 6.5), 50 mM NaCl, 0.1% sodium azide, 1mM DTT and 1 mM EDTA

#	Name	Isotope labeling	Concentration
1	SF1N	[U-15N]	100.0 ~ 600.0 uM
2	SF1N	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	SF1N	[U-13C; U-15N; U-2H]	100.0 ~ 600.0 uM
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	1 mM
7	sodium azide	natural abundance	0.1 %
8	EDTA	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.15 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2M09, Strand ID: A Detail

Release date

2013-01-27

Citation

Structure, phosphorylation and U2AF65 binding of the N-terminal domain of splicing factor 1 during 3'-splice site recognition
Zhang, Y., Madl, T., Bagdiul, I., Kern, T., Kang, H., Zou, P., Maeusbacher, N., Sieber, S., Kraemer, A., Sattler, M.
Nucleic Acids Res. (2013), 41, 1343-1354, PubMed 23175611 , DOI 10.1093/nar/gks1097 , Abstract

Related entities 1. SF1N, : 1 : 9 : 21 entities Detail

Interaction partners 1. SF1N, : 158 interactors Detail

More details for 158 interactors identified by 17 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM sodium phosphate (pH 6.5), 50 mM NaCl, 0.1% sodium azide, 1mM DTT and 1 mM EDTA

#	Name	Isotope labeling	Concentration
1	SF1N	[U-15N]	100.0 ~ 600.0 uM
2	SF1N	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	SF1N	[U-13C; U-15N; U-2H]	100.0 ~ 600.0 uM
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	1 mM
7	sodium azide	natural abundance	0.1 %
8	EDTA	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SF1N	[U-15N]	100.0 ~ 600.0 uM
2	SF1N	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	SF1N	[U-13C; U-15N; U-2H]	100.0 ~ 600.0 uM
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	1 mM
7	sodium azide	natural abundance	0.1 %
8	EDTA	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SF1N	[U-15N]	100.0 ~ 600.0 uM
2	SF1N	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	SF1N	[U-13C; U-15N; U-2H]	100.0 ~ 600.0 uM
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	1 mM
7	sodium azide	natural abundance	0.1 %
8	EDTA	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SF1N	[U-15N]	100.0 ~ 600.0 uM
2	SF1N	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	SF1N	[U-13C; U-15N; U-2H]	100.0 ~ 600.0 uM
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	1 mM
7	sodium azide	natural abundance	0.1 %
8	EDTA	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

5 3D HNCA

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SF1N	[U-15N]	100.0 ~ 600.0 uM
2	SF1N	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	SF1N	[U-13C; U-15N; U-2H]	100.0 ~ 600.0 uM
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	1 mM
7	sodium azide	natural abundance	0.1 %
8	EDTA	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

6 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SF1N	[U-15N]	100.0 ~ 600.0 uM
2	SF1N	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	SF1N	[U-13C; U-15N; U-2H]	100.0 ~ 600.0 uM
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	1 mM
7	sodium azide	natural abundance	0.1 %
8	EDTA	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SF1N	[U-15N]	100.0 ~ 600.0 uM
2	SF1N	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	SF1N	[U-13C; U-15N; U-2H]	100.0 ~ 600.0 uM
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	1 mM
7	sodium azide	natural abundance	0.1 %
8	EDTA	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SF1N	[U-15N]	100.0 ~ 600.0 uM
2	SF1N	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	SF1N	[U-13C; U-15N; U-2H]	100.0 ~ 600.0 uM
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	1 mM
7	sodium azide	natural abundance	0.1 %
8	EDTA	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SF1N	[U-15N]	100.0 ~ 600.0 uM
2	SF1N	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	SF1N	[U-13C; U-15N; U-2H]	100.0 ~ 600.0 uM
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	1 mM
7	sodium azide	natural abundance	0.1 %
8	EDTA	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

10 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	SF1N	[U-15N]	100.0 ~ 600.0 uM
2	SF1N	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	SF1N	[U-13C; U-15N; U-2H]	100.0 ~ 600.0 uM
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	DTT	natural abundance	1 mM
7	sodium azide	natural abundance	0.1 %
8	EDTA	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	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_18802_2m09.nef
Input source #2: Coordindates	2m09.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

----30--------40--------50--------60--------70--------80--------90-------100-------110-------120----
GAMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPNPEDRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPNPEDRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFK
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

---130-------140-----
PPADYKPPATRVSDKVMIPQD
|||||||||||||||||||||
PPADYKPPATRVSDKVMIPQD
-------110-------120-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	121	0	0	100.0

Content subtype: combined_18802_2m09.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1357		96.7 (chain: A, length: 121)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	2692 (1)	noe	99.2 (chain: A, length: 121)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	76 (1)	hbond	38.0 (chain: A, length: 121)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	189 (189)	.	93.4 (chain: A, length: 121)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 96.7%

----30--------40--------50--------60--------70--------80--------90-------100-------110-------120----
GAMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPNPEDRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFK
||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| ||||||||||||| |||||||||||||| |
GAMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDL.RKLRTGDLGIPPNPEDRSPSPEPIYNSEGKR.NTREFRTRKKLEE.RHNLITEMVALNPD.K

---130-------140-----
PPADYKPPATRVSDKVMIPQD
|||||||||||||||||||||
PPADYKPPATRVSDKVMIPQD

Total number of assignments
- ¹H chemical shifts: 713
- ¹³C chemical shifts: 532
- ¹⁵N chemical shifts: 112

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
29	GLN	CD	180.447
48	GLN	CD	179.961
55	GLN	CD	179.945
57	GLN	CD	179.334
60	ASP	CG	178.873
75	ASN	CG	177.156
78	ASP	CG	179.982
88	ASN	CG	176.888
95	ASN	CG	177.15
111	ASN	CG	175.738
120	ASN	CG	177.922
122	ASP	CG	179.922
128	ASP	CG	181.265
144	GLN	CD	180.909

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	771	713	92.5
¹³C chemical shifts	556	518	93.2
¹⁵N chemical shifts	126	112	88.9

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	232	222	95.7
¹³C chemical shifts	242	230	95.0
¹⁵N chemical shifts	105	100	95.2

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	539	491	91.1
¹³C chemical shifts	314	288	91.7
¹⁵N chemical shifts	21	12	57.1

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	58	90.6
¹³C chemical shifts	64	57	89.1

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	19	79.2
¹³C chemical shifts	24	18	75.0

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: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 99.2%
- Total number of restraints: 2685
- Weight of restraints: 1.0 (2685)
- Potential type of restraints: square-well-parabolic (2685)
- Range of distance target values: 1.15, 2.75 (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: 121, Sequence coverage: 38.0%
  - Total number of restraints: 76
  - Weight of restraints: 1.0 (76)
  - Potential type of restraints: square-well-parabolic (76)
  - Range of distance target values: 1.2, 1.7 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 93.4%
- Total number of restraints: 189
- Total number of restraints per polymer type: 189
- Weight of restraints: 1.0 (189)
- Potential type of restraints: square-well-parabolic (189)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords RRM, SF1, spliceosome assembly, U2AF65, UHM, ULM

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Found 1 Document (2.681 seconds)

BMRB: 18802

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. SF1N, : 1 : 9 : 21 entities Detail

Interaction partners 1. SF1N, : 158 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail