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Found 1 Document (1.007 seconds)

BMRB: 34155

5OBN

NMR solution structure of U11/U12 65K protein's C-terminal RRM domain (381-516)

Authors

Norppa, A.J., Kauppala, T.M., Heikkinen, H.A., Verma, B., Iwai, H., Frilander, M.J.

Assembly

RNA-binding protein 40

Entity

1. RNA-binding protein 40 (polymer, Thiol state: all free), 136 monomers, 15767.04 Da Detail

SDEMPSECIS RRELEKGRIS REEMETLSVF RSYEPGEPNC RIYVKNLAKH VQEKDLKYIF GRYVDFSSET QRIMFDIRLM KEGRMKGQAF IGLPNEKAAA KALKEANGYV LFGKPMVVQF ARSARPKQDP KEGKRK

Formula weight

15767.04 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.0 %, Completeness (bb): 98.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.0 % (1576 of 1659)	94.7 % (840 of 887)	94.8 % (601 of 634)	97.8 % (135 of 138)
Backbone	98.5 % (790 of 802)	97.8 % (268 of 274)	99.0 % (395 of 399)	98.4 % (127 of 129)
Sidechain	92.7 % (912 of 984)	93.3 % (572 of 613)	91.7 % (332 of 362)	88.9 % (8 of 9)
Aromatic	70.2 % (80 of 114)	84.2 % (48 of 57)	56.1 % (32 of 57)
Methyl	100.0 % (110 of 110)	100.0 % (55 of 55)	100.0 % (55 of 55)

1. entity 1

SDEMPSECIS RRELEKGRIS REEMETLSVF RSYEPGEPNC RIYVKNLAKH VQEKDLKYIF GRYVDFSSET QRIMFDIRLM KEGRMKGQAF IGLPNEKAAA KALKEANGYV LFGKPMVVQF ARSARPKQDP KEGKRK

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

LACS Plot; CA

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

Referencing offset: -0.18 ppm, Outliers: 4 Detail

LACS Plot; CB

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

Referencing offset: -0.18 ppm, Outliers: 4 Detail

LACS Plot; HA

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

Referencing offset: 0.03 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.12 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5OBN, Strand ID: A Detail

Release date

2018-01-15

Citation

Mutations in the U11/U12-65K protein associated with isolated growth hormone deficiency lead to structural destabilization and impaired binding of U12 snRNA
Norppa, A.J., Kauppala, T.M., Heikkinen, H.A., Verma, B., Iwai, H., Frilander, M.J.
RNA (2018), 24, 396-409, PubMed 29255062 , DOI 10.1261/rna.062844.117 , Abstract

Related entities 1. RNA-binding protein 40, : 1 : 3 : 1 : 42 entities Detail

Interaction partners 1. RNA-binding protein 40, : 7 interactors Detail

More details for 7 interactors identified by 6 citations

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

2 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

3 3D HNCA

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

4 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

5 3D HN(COCA)CB

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

6 HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

7 HN(CA)CO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

8 CON

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

9 CACO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

10 (H)CCCONH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

11 H(CCO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

12 HBHACONH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

13 HCCH-COSY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

14 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

15 CBCGCDHD

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

16 CBCGCDCEHE

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

17 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

18 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.3 K, pH 6.0, Details 0.2 mM [U-100% 13C; U-100% 15N] U11/U12 65K C-terminal RRM, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	U11/U12 65K C-terminal RRM	[U-100% 13C; U-100% 15N]		0.2 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34155_5obn.nef
Input source #2: Coordindates	5obn.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

-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480
SDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------490-------500-------510------
KALKEANGYVLFGKPMVVQFARSARPKQDPKEGKRK
||||||||||||||||||||||||||||||||||||
KALKEANGYVLFGKPMVVQFARSARPKQDPKEGKRK
-------110-------120-------130------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	136	0	0	100.0

Content subtype: combined_34155_5obn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1592		100.0 (chain: A, length: 136)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3772 (1)	noe	99.3 (chain: A, length: 136)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 100.0%

-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480
SDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA

-------490-------500-------510------
KALKEANGYVLFGKPMVVQFARSARPKQDPKEGKRK
||||||||||||||||||||||||||||||||||||
KALKEANGYVLFGKPMVVQFARSARPKQDPKEGKRK

Total number of assignments
- ¹³C chemical shifts: 607
- ¹H chemical shifts: 846
- ¹⁵N chemical shifts: 139

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
385	PRO	N	135.033
415	PRO	N	135.242
418	PRO	N	137.229
432	GLN	CD	180.911
451	GLN	CD	179.07
468	GLN	CD	180.349
474	PRO	N	127.169
495	PRO	N	137.126
499	GLN	CD	180.068
506	PRO	N	137.179
508	GLN	CD	180.583
510	PRO	N	137.559

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	634	602	95.0
¹H chemical shifts	887	846	95.4
¹⁵N chemical shifts	151	132	87.4

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	272	271	99.6
¹H chemical shifts	274	268	97.8
¹⁵N chemical shifts	129	124	96.1

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	362	331	91.4
¹H chemical shifts	613	578	94.3
¹⁵N chemical shifts	22	8	36.4

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	61	61	100.0
¹H chemical shifts	61	61	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	57	32	56.1
¹H chemical shifts	57	49	86.0

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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 99.3%
- Total number of restraints: 3772
- Weight of restraints: 1.0 (3772)
- Potential type of restraints: upper-bound-parabolic (3772)
- Range of distance target values: 2.25, 6.37 (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

Keywords Minor spliceosome, RNA binding, SPLICING

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Found 1 Document (1.007 seconds)

BMRB: 34155

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. RNA-binding protein 40, : 1 : 3 : 1 : 42 entities Detail

Interaction partners 1. RNA-binding protein 40, : 7 interactors Detail

Experiments performed 18 experiments Detail

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NMR combined restraints 3 contents Detail