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Found 1 Document (7.51 seconds)

BMRB: 17622

2YH0

Solution structure of the closed conformation of human U2AF65 tandem RRM1 and RRM2 domains

Authors

Mackereth, C.D., Madl, T., Simon, B., Zanier, K., Gasch, A., Sattler, M.

Assembly

Solution structure of the closed conformation of human U2AF65 tandem RRM1 and RRM2 domains

Entity

1. Solution structure of the closed conformation of human U2AF65 tandem RRM1 and RRM2 domains (polymer, Thiol state: all free), 198 monomers, 21491.33 Da Detail

GAMARRLYVG NIPFGITEEA MMDFFNAQMR LGGLTQAPGN PVLAVQINQD KNFAFLEFRS VDETTQAMAF DGIIFQGQSL KIRRPHDYQP LPGMSENPSV YVPGVVSTVV PDSAHKLFIG GLPNYLNDDQ VKELLTSFGP LKAFNLVKDS ATGLSKGYAF CEYVDINVTD QAIAGLNGMQ LGDKKLLVQR ASVGAKNA

Formula weight

21491.33 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

MODIFIED ARIA

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.9 %, Completeness: 70.3 %, Completeness (bb): 73.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	70.3 % (1599 of 2275)	71.6 % (844 of 1178)	63.7 % (564 of 886)	90.5 % (191 of 211)
Backbone	73.1 % (852 of 1166)	83.4 % (337 of 404)	59.3 % (341 of 575)	93.0 % (174 of 187)
Sidechain	69.3 % (892 of 1288)	65.5 % (507 of 774)	75.1 % (368 of 490)	70.8 % (17 of 24)
Aromatic	69.3 % (122 of 176)	76.1 % (67 of 88)	62.5 % (55 of 88)
Methyl	81.6 % (186 of 228)	81.6 % (93 of 114)	81.6 % (93 of 114)

1. HUMAN U2AF65

Show sample condition

Sample

Solvent system 90% water/10% D2O, Pressure 1.000 atm, Temperature 295.000 K, pH 6.500, Details protein 0.2 mM

#	Name	Isotope labeling	Concentration
1	HUMAN_U2AF65	[U-13C; U-15N]	0.2 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate	natural abundance	20 mM
5	NaCl	natural abundance	50 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	external	indirect	0.2514495
¹H	HDO	protons	4.8 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	external	indirect	0.1013291

Referencing offset: 0.17 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	external	indirect	0.2514495
¹H	HDO	protons	4.8 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	external	indirect	0.1013291

Referencing offset: 0.17 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	external	indirect	0.2514495
¹H	HDO	protons	4.8 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	external	indirect	0.1013291

Referencing offset: 0.13 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2YH0, Strand ID: A Detail

Release date

2011-08-02

Citation

Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF
Mackereth, C.D., Madl, T., Bonnal, S., Simon, B., Zanier, K., Gasch, A., Rybin, V., Valcarcel, J., Sattler, M.
Nature (2011), 475, 408-411, PubMed 21753750 , DOI 10.1038/nature10171 , Abstract

Related entities 1. Solution structure of the closed conformation of human U2AF65 tandem RRM1 and RRM2 domains, : 1 : 1 : 16 : 177 entities Detail

Interaction partners 1. Solution structure of the closed conformation of human U2AF65 tandem RRM1 and RRM2 domains, : 20 interactors Detail

More details for 20 interactors identified by 3 citations

Experiments performed 2 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17622_2yh0.nef
Input source #2: Coordindates	2yh0.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

---150-------160-------170-------180-------190-------200-------210-------220-------230-------240----
GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

---250-------260-------270-------280-------290-------300-------310-------320-------330-------340--
YVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
YVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNA
-------110-------120-------130-------140-------150-------160-------170-------180-------190--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	198	0	0	100.0

Content subtype: combined_17622_2yh0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1527		93.9 (chain: A, length: 198)
1	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	101 (1)	hbond	34.8 (chain: A, length: 198)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	170 (170)	.	63.6 (chain: A, length: 198)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 93.9%
- Total number of assignments
  - ¹H chemical shifts: 843
  - ¹³C chemical shifts: 497
  - ¹⁵N chemical shifts: 187
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1178	751	63.8
¹³C chemical shifts	886	497	56.1
¹⁵N chemical shifts	218	187	85.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	404	317	78.5
¹³C chemical shifts	396	144	36.4
¹⁵N chemical shifts	187	171	91.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	774	434	56.1
¹³C chemical shifts	490	353	72.0
¹⁵N chemical shifts	31	16	51.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	121	94	77.7
¹³C chemical shifts	121	96	79.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	88	60	68.2
¹³C chemical shifts	88	47	53.4

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_5
- Status: OK
- Experiment type: hbond
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 34.8%
- Total number of restraints: 101
- Weight of restraints: 1.0 (101)
- Potential type of restraints: square-well-parabolic (101)
- Range of distance target values: 2.05, 3.05 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 63.6%
- Total number of restraints: 170
- Total number of restraints per polymer type: 170
- Weight of restraints: 1.0 (170)
- Potential type of restraints: square-well-parabolic (170)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords human, model, NMR, pre-mRNA splicing, protein structure, RNA-binding protein, RNA- BINDING PROTEIN

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Found 1 Document (7.51 seconds)

BMRB: 17622

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Solution structure of the closed conformation of human U2AF65 tandem RRM1 and RRM2 domains, : 1 : 1 : 16 : 177 entities Detail

Interaction partners 1. Solution structure of the closed conformation of human U2AF65 tandem RRM1 and RRM2 domains, : 20 interactors Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail