BMRB Entry 34816

Name: Solution structure of a chimeric U2AF2 RRM2 / FUBP1 N-Box
Published: 2023-07-21

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PDB ID: 8p25
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34816
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of a chimeric U2AF2 RRM2 / FUBP1 N-Box

Deposition date:

2023-05-14

Original release date:

2023-07-21

Authors:

Hipp, C.; Sattler, M.

Citation:

Citation: Ebersberger, Stefanie; Hipp, Clara; Mulorz, Miriam; Buchbender, Andreas; Hubrich, Dalmira; Kang, Hyun-Seo; Martinez-Lumbreras, Santiago; Kristofori, Panajot; Sutandy, F.; Llacsahuanga Allcca, Lidia; Schonfeld, Jonas; Bakisoglu, Cem; Busch, Anke; Hanel, Heike; Tretow, Kerstin; Welzel, Mareen; Di Liddo, Antonella; Mockel, Martin; Zarnack, Kathi; Ebersberger, Ingo; Legewie, Stefan; Luck, Katja; Sattler, Michael; Konig, Julian. "FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns" Mol. Cell 83, 2653-2672 (2023).
PubMed: 37506698

Assembly members:

Assembly members:
entity_1, polymer, 160 residues, 16296.167 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: pETM11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AMDYQPLPGMSENPSVYVPG VVSTVVPDSAHKLFIGGLPN YLNDDQVKELLTSFGPLKAF NLVKDSATGLSKGYAFCEYV DINVTDQAIAGLNGMQLGDK KLLVQRASVGAKNAGSGGSG SSGSGGSGGGVNDAFKDALQ RARQIAAKIGGDAGTSLNSN

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	471
15N chemical shifts	162
1H chemical shifts	985

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 160 residues - 16296.167 Da.

1	ALA	MET	ASP	TYR	GLN	PRO	LEU	PRO	GLY	MET
2	SER	GLU	ASN	PRO	SER	VAL	TYR	VAL	PRO	GLY
3	VAL	VAL	SER	THR	VAL	VAL	PRO	ASP	SER	ALA
4	HIS	LYS	LEU	PHE	ILE	GLY	GLY	LEU	PRO	ASN
5	TYR	LEU	ASN	ASP	ASP	GLN	VAL	LYS	GLU	LEU
6	LEU	THR	SER	PHE	GLY	PRO	LEU	LYS	ALA	PHE
7	ASN	LEU	VAL	LYS	ASP	SER	ALA	THR	GLY	LEU
8	SER	LYS	GLY	TYR	ALA	PHE	CYS	GLU	TYR	VAL
9	ASP	ILE	ASN	VAL	THR	ASP	GLN	ALA	ILE	ALA
10	GLY	LEU	ASN	GLY	MET	GLN	LEU	GLY	ASP	LYS
11	LYS	LEU	LEU	VAL	GLN	ARG	ALA	SER	VAL	GLY
12	ALA	LYS	ASN	ALA	GLY	SER	GLY	GLY	SER	GLY
13	SER	SER	GLY	SER	GLY	GLY	SER	GLY	GLY	GLY
14	VAL	ASN	ASP	ALA	PHE	LYS	ASP	ALA	LEU	GLN
15	ARG	ALA	ARG	GLN	ILE	ALA	ALA	LYS	ILE	GLY
16	GLY	ASP	ALA	GLY	THR	SER	LEU	ASN	SER	ASN

Samples:

sample_1: Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-box, [U-100% 13C; U-100% 15N], 0.6 mM; NaCl 50 mM

sample_2: Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-box, [U-100% 13C; U-100% 15N], 0.6 mM; NaCl 50 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACO	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
HBCBCGCDHD	sample_2	isotropic	sample_conditions_1
HBCBCGCDCEHE	sample_2	isotropic	sample_conditions_1

Software:

ARIA v2.3, Linge, O'Donoghue and Nilges - refinement

CYANA v3.98.15, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRFAM-SPARKY, Lee W., Tonelli M., Markley J. L. - chemical shift assignment, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TopSpin, Bruker Biospin - processing

TALOS+, Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Bax - geometry optimization

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE III 900 MHz
Bruker AVANCE III HD 950 MHz
Bruker AVANCE III 500 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

1	ALA	MET	ASP	TYR	GLN	PRO	LEU	PRO	GLY	MET
2	SER	GLU	ASN	PRO	SER	VAL	TYR	VAL	PRO	GLY
3	VAL	VAL	SER	THR	VAL	VAL	PRO	ASP	SER	ALA
4	HIS	LYS	LEU	PHE	ILE	GLY	GLY	LEU	PRO	ASN
5	TYR	LEU	ASN	ASP	ASP	GLN	VAL	LYS	GLU	LEU
6	LEU	THR	SER	PHE	GLY	PRO	LEU	LYS	ALA	PHE
7	ASN	LEU	VAL	LYS	ASP	SER	ALA	THR	GLY	LEU
8	SER	LYS	GLY	TYR	ALA	PHE	CYS	GLU	TYR	VAL
9	ASP	ILE	ASN	VAL	THR	ASP	GLN	ALA	ILE	ALA
10	GLY	LEU	ASN	GLY	MET	GLN	LEU	GLY	ASP	LYS
11	LYS	LEU	LEU	VAL	GLN	ARG	ALA	SER	VAL	GLY
12	ALA	LYS	ASN	ALA	GLY	SER	GLY	GLY	SER	GLY
13	SER	SER	GLY	SER	GLY	GLY	SER	GLY	GLY	GLY
14	VAL	ASN	ASP	ALA	PHE	LYS	ASP	ALA	LEU	GLN
15	ARG	ALA	ARG	GLN	ILE	ALA	ALA	LYS	ILE	GLY
16	GLY	ASP	ALA	GLY	THR	SER	LEU	ASN	SER	ASN

1	ALA	MET	ASP	TYR	GLN	PRO	LEU	PRO	GLY	MET
2	SER	GLU	ASN	PRO	SER	VAL	TYR	VAL	PRO	GLY
3	VAL	VAL	SER	THR	VAL	VAL	PRO	ASP	SER	ALA
4	HIS	LYS	LEU	PHE	ILE	GLY	GLY	LEU	PRO	ASN
5	TYR	LEU	ASN	ASP	ASP	GLN	VAL	LYS	GLU	LEU
6	LEU	THR	SER	PHE	GLY	PRO	LEU	LYS	ALA	PHE
7	ASN	LEU	VAL	LYS	ASP	SER	ALA	THR	GLY	LEU
8	SER	LYS	GLY	TYR	ALA	PHE	CYS	GLU	TYR	VAL
9	ASP	ILE	ASN	VAL	THR	ASP	GLN	ALA	ILE	ALA
10	GLY	LEU	ASN	GLY	MET	GLN	LEU	GLY	ASP	LYS
11	LYS	LEU	LEU	VAL	GLN	ARG	ALA	SER	VAL	GLY
12	ALA	LYS	ASN	ALA	GLY	SER	GLY	GLY	SER	GLY
13	SER	SER	GLY	SER	GLY	GLY	SER	GLY	GLY	GLY
14	VAL	ASN	ASP	ALA	PHE	LYS	ASP	ALA	LEU	GLN
15	ARG	ALA	ARG	GLN	ILE	ALA	ALA	LYS	ILE	GLY
16	GLY	ASP	ALA	GLY	THR	SER	LEU	ASN	SER	ASN

1	ALA	MET	ASP	TYR	GLN	PRO	LEU	PRO	GLY	MET
2	SER	GLU	ASN	PRO	SER	VAL	TYR	VAL	PRO	GLY
3	VAL	VAL	SER	THR	VAL	VAL	PRO	ASP	SER	ALA
4	HIS	LYS	LEU	PHE	ILE	GLY	GLY	LEU	PRO	ASN
5	TYR	LEU	ASN	ASP	ASP	GLN	VAL	LYS	GLU	LEU
6	LEU	THR	SER	PHE	GLY	PRO	LEU	LYS	ALA	PHE
7	ASN	LEU	VAL	LYS	ASP	SER	ALA	THR	GLY	LEU
8	SER	LYS	GLY	TYR	ALA	PHE	CYS	GLU	TYR	VAL
9	ASP	ILE	ASN	VAL	THR	ASP	GLN	ALA	ILE	ALA
10	GLY	LEU	ASN	GLY	MET	GLN	LEU	GLY	ASP	LYS
11	LYS	LEU	LEU	VAL	GLN	ARG	ALA	SER	VAL	GLY
12	ALA	LYS	ASN	ALA	GLY	SER	GLY	GLY	SER	GLY
13	SER	SER	GLY	SER	GLY	GLY	SER	GLY	GLY	GLY
14	VAL	ASN	ASP	ALA	PHE	LYS	ASP	ALA	LEU	GLN
15	ARG	ALA	ARG	GLN	ILE	ALA	ALA	LYS	ILE	GLY
16	GLY	ASP	ALA	GLY	THR	SER	LEU	ASN	SER	ASN