BMRBj - BMREntryMaster

Found 1 Document (0.706 seconds)

BMRB: 17623

2YH1

MODEL OF HUMAN U2AF65 TANDEM RRM1 AND RRM2 DOMAINS WITH EIGHT-SITE URIDINE BINDING

Authors

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

Assembly

Model of human U2AF65 tandem RRM1 and RRM2 domains with eight-site uridine binding

Entity

1. HUMAN U2AF65 (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

2. 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3' (polymer, Thiol state: not present), 9 monomers, 2773.507 Da Detail

UUUUUUUUU

Total weight

24264.838 Da

Max. entity 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: 89.9 %, Completeness: 57.1 %, Completeness (bb): 62.8 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	57.1 % (1387 of 2428)	61.0 % (768 of 1259)	45.2 % (429 of 949)	86.4 % (190 of 220)
Backbone	62.8 % (795 of 1265)	70.3 % (322 of 458)	47.7 % (296 of 620)	94.7 % (177 of 187)
Sidechain	53.6 % (719 of 1342)	55.8 % (447 of 801)	51.0 % (259 of 508)	39.4 % (13 of 33)
Aromatic	18.7 % (43 of 230)	37.4 % (43 of 115)	0.0 % (0 of 106)	0.0 % (0 of 9)
Methyl	74.1 % (169 of 228)	74.6 % (85 of 114)	73.7 % (84 of 114)

1. HUMAN U2AF65

2. 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3'

UUUUUUUUU

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 RNA 0.24 mM

#	Name	Isotope labeling	Concentration
1	HUMAN_U2AF65	[U-13C; U-15N]	0.2 mM
2	RNA	natural abundance	0.24 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %
5	sodium phosphate	natural abundance	20 mM
6	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	water protons	4.8 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	external	indirect	0.1013291

Referencing offset: 0.15 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	water protons	4.8 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	external	indirect	0.1013291

Referencing offset: 0.15 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	water protons	4.8 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	external	indirect	0.1013291

Referencing offset: 0.1 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2YH1, 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. HUMAN U2AF65, : 1 : 1 : 16 : 177 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17623_2yh1.nef
Input source #2: Coordindates	2yh1.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	Error

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--------

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

---------
UUUUUUUUU
|||||||||
UUUUUUUUU

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	198	0	0	100.0
B	B	9	0	0	100.0

Content subtype: combined_17623_2yh1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1393		91.4 (chain: A, length: 198)
1	Distance restraints	CNS/XPLOR_distance_constraints_8	Error	1075 (1)	undefined	21.2 (chain: A, length: 198), 88.9 (chain: B, length: 9)
2	Distance restraints	CNS/XPLOR_distance_constraints_7	OK	81 (1)	hbond	53.5 (chain: A, length: 198)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	248 (248)	.	76.3 (chain: A, length: 198)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	102 (102)	.	35.4 (chain: A, length: 198)
2	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	81 (81)	.	33.8 (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: 91.4%
- Total number of assignments
  - ¹H chemical shifts: 834
  - ¹⁵N chemical shifts: 184
  - ¹³C chemical shifts: 375
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1178	741	62.9
¹⁵N chemical shifts	218	184	84.4
¹³C chemical shifts	886	375	42.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	404	310	76.7
¹⁵N chemical shifts	187	171	91.4
¹³C chemical shifts	396	129	32.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	774	431	55.7
¹⁵N chemical shifts	31	13	41.9
¹³C chemical shifts	490	246	50.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	121	86	71.1
¹³C chemical shifts	121	86	71.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	88	43	48.9
¹³C chemical shifts	88	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_8
- Status: Error
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 21.2%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 88.9%
- Total number of restraints: 1075
- Weight of restraints: 1.0 (1075)
- Potential type of restraints: square-well-parabolic (1075)
- Range of distance target values: 2.13, 4.99 (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
- Saveframe: CNS/XPLOR_distance_constraints_7
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 53.5%
  - Total number of restraints: 81
  - Weight of restraints: 1.0 (81)
  - Potential type of restraints: square-well-parabolic (81)
  - Range of distance target values: 2.05, 2.05 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 76.3%
- Total number of restraints: 248
- Total number of restraints per polymer type: 248
- Weight of restraints: 1.0 (248)
- Potential type of restraints: square-well-parabolic (248)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 35.4%
- Total number of restraints: 102
- Potential type of restraints: undefined (102)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
- Saveframe: CNS/XPLOR_dipolar_coupling_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 198, Sequence coverage: 33.8%
  - Total number of restraints: 81
  - Potential type of restraints: undefined (81)
  - Range of observed RDC values: 100.0, -100.0 (Hz)
  - RDC restraints per residue

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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.706 seconds)

BMRB: 17623

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HUMAN U2AF65, : 1 : 1 : 16 : 177 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail