BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	92.3 % (1104 of 1196)	91.8 % (570 of 621)	91.9 % (433 of 471)	97.1 % (101 of 104)
Backbone	95.1 % (559 of 588)	96.5 % (194 of 201)	93.6 % (276 of 295)	96.7 % (89 of 92)
Sidechain	90.4 % (634 of 701)	89.5 % (376 of 420)	91.4 % (246 of 269)	100.0 % (12 of 12)
Aromatic	84.1 % (111 of 132)	87.9 % (58 of 66)	80.0 % (52 of 65)	100.0 % (1 of 1)
Methyl	97.3 % (107 of 110)	96.4 % (53 of 55)	98.2 % (54 of 55)

1. NUCLEAR AND CYTOPLASMIC POLYADENYLATED RNA-BINDING PUB1

GSQTIGLPPQ VNPQAVDHII RSAPPRVTTA YIGNIPHFAT EADLIPLFQN FGFILDFKHY PEKGCCFIKY DTHEQAAVCI VALANFPFQG RNLRTGWGKE R

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.3MM [U-100% 15N] PUB1P RRM3

#	Name	Isotope labeling	Concentration
1	PUB1 RRM3	[U-99% 15N]	0.3 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	25 mM
4	DTT	natural abundance	0.5 mM
5	DSS	natural abundance	0.01 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.01MM DSS

#	Name	Isotope labeling	Concentration
8	PUB1 RRM3	natural abundance	0.3 mM
9	potassium phosphate	natural abundance	25 mM
10	sodium chloride	natural abundance	25 mM
11	DTT	natural abundance	0.5 mM
12	DSS	natural abundance	0.01 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
15	PUB1 RRM3	natural abundance	0.3 mM
16	potassium phosphate	natural abundance	25 mM
17	sodium chloride	natural abundance	25 mM
18	DTT	natural abundance	0.5 mM
19	DSS	natural abundance	0.1 mM
20	D2O	natural abundance	100 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
21	PUB1 RRM3	[U-99% 13C; U-99% 15N]	0.3 mM
22	potassium phosphate	natural abundance	25 mM
23	sodium chloride	natural abundance	25 mM
24	DTT	natural abundance	0.5 mM
25	DSS	natural abundance	0.1 mM
26	H2O	natural abundance	90 %
27	D2O	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.01 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.19 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LA4, Strand ID: A Detail

Release date

2012-02-29

Citation

Pub1p C-terminal RRM domain interacts with Tif4631p through a conserved region neighbouring the Pab1p binding site
Santiveri, C.M., Mirassou, Y., Rico-Lastres, P.R., Martinez-Lumbreras, S.M., Perez-Canadillas, J.M.
PLoS One (2011), 6, e24481-e24481, PubMed 21931728 , DOI 10.1371/journal.pone.0024481 , Abstract

Related entities 1. NUCLEAR AND CYTOPLASMIC POLYADENYLATED RNA-BINDING PUB1, : 1 : 3 : 88 entities Detail

Interaction partners 1. NUCLEAR AND CYTOPLASMIC POLYADENYLATED RNA-BINDING PUB1, : 19 interactors Detail

More details for 19 interactors identified by 4 citations

Experiments performed 14 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.01MM DSS

#	Name	Isotope labeling	Concentration
8	PUB1 RRM3	natural abundance	0.3 mM
9	potassium phosphate	natural abundance	25 mM
10	sodium chloride	natural abundance	25 mM
11	DTT	natural abundance	0.5 mM
12	DSS	natural abundance	0.01 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

2 3D 1H-15N NOESY 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.3MM [U-100% 15N] PUB1P RRM3

#	Name	Isotope labeling	Concentration
1	PUB1 RRM3	[U-99% 15N]	0.3 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	25 mM
4	DTT	natural abundance	0.5 mM
5	DSS	natural abundance	0.01 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 3D HNCO

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
21	PUB1 RRM3	[U-99% 13C; U-99% 15N]	0.3 mM
22	potassium phosphate	natural abundance	25 mM
23	sodium chloride	natural abundance	25 mM
24	DTT	natural abundance	0.5 mM
25	DSS	natural abundance	0.1 mM
26	H2O	natural abundance	90 %
27	D2O	natural abundance	10 %

4 3D HN(CA)CO

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
21	PUB1 RRM3	[U-99% 13C; U-99% 15N]	0.3 mM
22	potassium phosphate	natural abundance	25 mM
23	sodium chloride	natural abundance	25 mM
24	DTT	natural abundance	0.5 mM
25	DSS	natural abundance	0.1 mM
26	H2O	natural abundance	90 %
27	D2O	natural abundance	10 %

5 3D HNCA

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
21	PUB1 RRM3	[U-99% 13C; U-99% 15N]	0.3 mM
22	potassium phosphate	natural abundance	25 mM
23	sodium chloride	natural abundance	25 mM
24	DTT	natural abundance	0.5 mM
25	DSS	natural abundance	0.1 mM
26	H2O	natural abundance	90 %
27	D2O	natural abundance	10 %

6 3D HN(CO)CA

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
21	PUB1 RRM3	[U-99% 13C; U-99% 15N]	0.3 mM
22	potassium phosphate	natural abundance	25 mM
23	sodium chloride	natural abundance	25 mM
24	DTT	natural abundance	0.5 mM
25	DSS	natural abundance	0.1 mM
26	H2O	natural abundance	90 %
27	D2O	natural abundance	10 %

7 3D CBCA(CO)NH

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
21	PUB1 RRM3	[U-99% 13C; U-99% 15N]	0.3 mM
22	potassium phosphate	natural abundance	25 mM
23	sodium chloride	natural abundance	25 mM
24	DTT	natural abundance	0.5 mM
25	DSS	natural abundance	0.1 mM
26	H2O	natural abundance	90 %
27	D2O	natural abundance	10 %

8 3D CBCANH

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
21	PUB1 RRM3	[U-99% 13C; U-99% 15N]	0.3 mM
22	potassium phosphate	natural abundance	25 mM
23	sodium chloride	natural abundance	25 mM
24	DTT	natural abundance	0.5 mM
25	DSS	natural abundance	0.1 mM
26	H2O	natural abundance	90 %
27	D2O	natural abundance	10 %

9 3D HC -TOCSY

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
21	PUB1 RRM3	[U-99% 13C; U-99% 15N]	0.3 mM
22	potassium phosphate	natural abundance	25 mM
23	sodium chloride	natural abundance	25 mM
24	DTT	natural abundance	0.5 mM
25	DSS	natural abundance	0.1 mM
26	H2O	natural abundance	90 %
27	D2O	natural abundance	10 %

10 2D 1H-1H NOESY

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
15	PUB1 RRM3	natural abundance	0.3 mM
16	potassium phosphate	natural abundance	25 mM
17	sodium chloride	natural abundance	25 mM
18	DTT	natural abundance	0.5 mM
19	DSS	natural abundance	0.1 mM
20	D2O	natural abundance	100 %

11 2D 1H-1H TOCSY

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.01MM DSS

#	Name	Isotope labeling	Concentration
8	PUB1 RRM3	natural abundance	0.3 mM
9	potassium phosphate	natural abundance	25 mM
10	sodium chloride	natural abundance	25 mM
11	DTT	natural abundance	0.5 mM
12	DSS	natural abundance	0.01 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

12 2D 1H-1H TOCSY

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
15	PUB1 RRM3	natural abundance	0.3 mM
16	potassium phosphate	natural abundance	25 mM
17	sodium chloride	natural abundance	25 mM
18	DTT	natural abundance	0.5 mM
19	DSS	natural abundance	0.1 mM
20	D2O	natural abundance	100 %

13 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.3MM [U-100% 15N] PUB1P RRM3

#	Name	Isotope labeling	Concentration
1	PUB1 RRM3	[U-99% 15N]	0.3 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	25 mM
4	DTT	natural abundance	0.5 mM
5	DSS	natural abundance	0.01 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

14 2D 1H-13C HSQC

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
21	PUB1 RRM3	[U-99% 13C; U-99% 15N]	0.3 mM
22	potassium phosphate	natural abundance	25 mM
23	sodium chloride	natural abundance	25 mM
24	DTT	natural abundance	0.5 mM
25	DSS	natural abundance	0.1 mM
26	H2O	natural abundance	90 %
27	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_17502_2la4.nef
Input source #2: Coordindates	2la4.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

----320-------330-------340-------350-------360-------370-------380-------390-------400-------410---
GSQTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSQTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-
R
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R
-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	101	0	0	100.0

Content subtype: combined_17502_2la4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1138		100.0 (chain: A, length: 101)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2677 (1)	noe	97.0 (chain: A, length: 101)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	129 (129)	.	87.1 (chain: A, length: 101)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 100.0%

----320-------330-------340-------350-------360-------370-------380-------390-------400-------410---
GSQTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSQTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE

-
R
|
R

Total number of assignments
- ¹H chemical shifts: 587
- ¹³C chemical shifts: 451
- ¹⁵N chemical shifts: 100

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
316	GLN	CD	180.578
323	GLN	CD	180.854
325	ASN	CG	176.906
327	GLN	CD	180.588
330	ASP	CG	179.279
347	ASN	CG	179.096
354	GLU	CD	182.89
356	ASP	CG	179.149
362	GLN	CD	179.82
363	ASN	CG	175.852
369	ASP	CG	179.652
375	GLU	CD	183.917
379	CYS	HG	0.999
383	TYR	HH	8.688
384	ASP	CG	178.187
385	THR	HG1	5.592
387	GLU	CD	184.026
388	GLN	CD	180.995
392	CYS	HG	1.233
398	ASN	CG	178.655
402	GLN	CD	179.354
408	THR	HG1	5.826
413	GLU	CD	183.972

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	621	582	93.7
¹³C chemical shifts	471	433	91.9
¹⁵N chemical shifts	109	100	91.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	201	196	97.5
¹³C chemical shifts	202	188	93.1
¹⁵N chemical shifts	92	88	95.7

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	420	386	91.9
¹³C chemical shifts	269	245	91.1
¹⁵N chemical shifts	17	12	70.6

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	55	55	100.0
¹³C chemical shifts	55	54	98.2

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	61	92.4
¹³C chemical shifts	65	51	78.5
¹⁵N chemical shifts	1	1	100.0

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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 97.0%
- Total number of restraints: 2665
- Weight of restraints: 1.0 (2665)
- Potential type of restraints: upper-bound-parabolic (2665)
- Range of distance target values: 2.92, 5.53 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 87.1%
- Total number of restraints: 129
- Total number of restraints per polymer type: 129
- Weight of restraints: 1.0 (129)
- Potential type of restraints: square-well-parabolic (129)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NUCLEUS, RNA-BINDING, RNA RECOGNITION, RRM, STRESS GRANULES, TRANSCRIPTION

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Found 1 Document (0.93 seconds)

BMRB: 17502

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. NUCLEAR AND CYTOPLASMIC POLYADENYLATED RNA-BINDING PUB1, : 1 : 3 : 88 entities Detail

Interaction partners 1. NUCLEAR AND CYTOPLASMIC POLYADENYLATED RNA-BINDING PUB1, : 19 interactors Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 4 contents Detail