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Found 1 Document (3.9 seconds)

BMRB: 18808

2M0G

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

Nterminal domain of splicing factor 1

Entity

1. Nterminal domain of splicing factor 1, entity 1 (polymer), 145 monomers, 16648.84 Da Detail

MATGANATPL DFPSKKRKRS RWNQDTMEQK TVIPGMPTVI PPGLTREQER AYIVQLQIED LTRKLRTGDL GIPPNPEDRS PSPEPIYNSE GKRLNTREFR TRKKLEEERH NLITEMVALN PDFKPPADYK PPATRVCDKV MIPQD

2. Nterminal domain of splicing factor 1, entity 2 (polymer), 104 monomers, 11962.49 Da Detail

GHPTEVLCLM NMVLPEELLD DEEYEEIVED VRDECSKYGL VKSIEIPRPV DGVEVPGCGK IFVEFTSVFD CQKAMQGLTG RKFANRVVVT KYCDPDSYHR RDFW

Total weight

28611.33 Da

Max. entity weight

16648.84 Da

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.6 %, Completeness: 38.6 %, Completeness (bb): 58.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	38.6 % (1138 of 2952)	27.3 % (426 of 1562)	43.7 % (501 of 1146)	86.5 % (211 of 244)
Backbone	58.3 % (843 of 1446)	51.3 % (250 of 487)	53.7 % (394 of 734)	88.4 % (199 of 225)
Sidechain	26.5 % (461 of 1742)	16.4 % (176 of 1075)	42.1 % (273 of 648)	63.2 % (12 of 19)
Aromatic	4.7 % (8 of 172)	7.0 % (6 of 86)	0.0 % (0 of 84)	100.0 % (2 of 2)
Methyl	79.3 % (192 of 242)	79.3 % (96 of 121)	79.3 % (96 of 121)

1. entity 1

MATGANATPL DFPSKKRKRS RWNQDTMEQK TVIPGMPTVI PPGLTREQER AYIVQLQIED LTRKLRTGDL GIPPNPEDRS PSPEPIYNSE GKRLNTREFR TRKKLEEERH NLITEMVALN PDFKPPADYK PPATRVCDKV MIPQD

2. entity 2

GHPTEVLCLM NMVLPEELLD DEEYEEIVED VRDECSKYGL VKSIEIPRPV DGVEVPGCGK IFVEFTSVFD CQKAMQGLTG RKFANRVVVT KYCDPDSYHR RDFW

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	entity	[U-15N]	100.0 ~ 600.0 uM
2	entity	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	entity	[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	sodium azide	natural abundance	0.1 %
7	DTT	natural abundance	1 mM
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: -0.31 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: -0.31 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2M0G, Strand ID: A, B 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. Nterminal domain of splicing factor 1, entity 1, : 5 : 21 entities Detail

Related entities 2. Nterminal domain of splicing factor 1, entity 2, : 1 : 7 : 3 : 118 entities Detail

Interaction partners 1. Nterminal domain of splicing factor 1, entity 1, : 158 interactors Detail

More details for 158 interactors identified by 18 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	entity	[U-15N]	100.0 ~ 600.0 uM
2	entity	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	entity	[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	sodium azide	natural abundance	0.1 %
7	DTT	natural abundance	1 mM
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	entity	[U-15N]	100.0 ~ 600.0 uM
2	entity	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	entity	[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	sodium azide	natural abundance	0.1 %
7	DTT	natural abundance	1 mM
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	entity	[U-15N]	100.0 ~ 600.0 uM
2	entity	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	entity	[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	sodium azide	natural abundance	0.1 %
7	DTT	natural abundance	1 mM
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	entity	[U-15N]	100.0 ~ 600.0 uM
2	entity	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	entity	[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	sodium azide	natural abundance	0.1 %
7	DTT	natural abundance	1 mM
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	entity	[U-15N]	100.0 ~ 600.0 uM
2	entity	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	entity	[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	sodium azide	natural abundance	0.1 %
7	DTT	natural abundance	1 mM
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	entity	[U-15N]	100.0 ~ 600.0 uM
2	entity	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	entity	[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	sodium azide	natural abundance	0.1 %
7	DTT	natural abundance	1 mM
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	entity	[U-15N]	100.0 ~ 600.0 uM
2	entity	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	entity	[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	sodium azide	natural abundance	0.1 %
7	DTT	natural abundance	1 mM
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	entity	[U-15N]	100.0 ~ 600.0 uM
2	entity	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	entity	[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	sodium azide	natural abundance	0.1 %
7	DTT	natural abundance	1 mM
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	entity	[U-15N]	100.0 ~ 600.0 uM
2	entity	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	entity	[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	sodium azide	natural abundance	0.1 %
7	DTT	natural abundance	1 mM
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	entity	[U-15N]	100.0 ~ 600.0 uM
2	entity	[U-13C; U-15N]	100.0 ~ 600.0 uM
3	entity	[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	sodium azide	natural abundance	0.1 %
7	DTT	natural abundance	1 mM
8	EDTA	natural abundance	1 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18808_2m0g.nef
Input source #2: Coordindates	2m0g.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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MATGANATPLDFPSKKRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPNPEDRSPSPEPIYNSEGKRLNTREFR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MATGANATPLDFPSKKRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPNPEDRSPSPEPIYNSEGKRLNTREFR

-------110-------120-------130-------140-----
TRKKLEEERHNLITEMVALNPDFKPPADYKPPATRVCDKVMIPQD
|||||||||||||||||||||||||||||||||||||||||||||
TRKKLEEERHNLITEMVALNPDFKPPADYKPPATRVCDKVMIPQD

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-
GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHR
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----
RDFW
||||
RDFW
----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	145	0	0	100.0
B	B	104	0	0	100.0

Content subtype: combined_18808_2m0g.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1061		84.1 (chain: A, length: 145), 100.0 (chain: B, length: 104)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	71 (1)	noe	10.3 (chain: A, length: 145), 10.6 (chain: B, length: 104)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	130 (130)	.	65.5 (chain: A, length: 145)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 84.1%
  - Entity_assembly_ID: B, Chain length: 104, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 384
  - ¹³C chemical shifts: 468
  - ¹⁵N chemical shifts: 209
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	929	222	23.9
¹³C chemical shifts	666	240	36.0
¹⁵N chemical shifts	155	112	72.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	278	136	48.9
¹³C chemical shifts	290	113	39.0
¹⁵N chemical shifts	127	101	79.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	651	86	13.2
¹³C chemical shifts	376	127	33.8
¹⁵N chemical shifts	28	11	39.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	50	69.4
¹³C chemical shifts	72	48	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	1	2.9
¹³C chemical shifts	34	0	0.0
¹⁵N chemical shifts	1	1	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
406	CYS	HG	2.597
442	CYS	HG	2.671

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	633	158	25.0
¹³C chemical shifts	480	228	47.5
¹⁵N chemical shifts	109	97	89.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	209	100	47.8
¹³C chemical shifts	208	99	47.6
¹⁵N chemical shifts	98	96	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	424	58	13.7
¹³C chemical shifts	272	129	47.4
¹⁵N chemical shifts	11	1	9.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	57	46	80.7
¹³C chemical shifts	57	47	82.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	5	9.8
¹³C chemical shifts	50	0	0.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 10.3%
  - Entity_assembly_ID: B, Chain length: 104, Sequence coverage: 10.6%
- 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, 52.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- 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: 145, Sequence coverage: 65.5%
- Total number of restraints: 130
- Total number of restraints per polymer type: 130
- Weight of restraints: 1.0 (130)
- Potential type of restraints: square-well-parabolic (130)
- 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 (3.9 seconds)

BMRB: 18808

Sample

Chemical shift reference

Chemical shift reference

Related entities 1. Nterminal domain of splicing factor 1, entity 1, : 5 : 21 entities Detail

Related entities 2. Nterminal domain of splicing factor 1, entity 2, : 1 : 7 : 3 : 118 entities Detail

Interaction partners 1. Nterminal domain of splicing factor 1, entity 1, : 158 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 4 contents Detail