BMRBj - BMREntryMaster

Found 1 Document (0.827 seconds)

BMRB: 30570

6NZ2

NMR solution structure of Bcd1p120-303 from Saccharomyces cerevisiae

Authors

Bragantini, B., Quinternet, M., Charpentier, B., Manival, X.

Assembly

Box C/D snoRNA protein 1

Entity

1. Box C/D snoRNA protein 1 (polymer), 188 monomers, 21830.96 Da Detail

GPHMRDSTEC QRIIRRGVNC LMLPKGMQRS SQNRSKWDKT MDLFVWSVEW ILCPMQEKGE KKELFKHVSH RIKETDFLVQ GMGKNVFQKC CEFYRLAGTS SCIEGEDGSE TKEERTQILQ KSGLKFYTKT FPYNTTHIMD SKKLVELAIH EKCIGELLKN TTVIEFPTIF VAMTEADLPE GYEVLHQE

Formula weight

21830.96 Da

Source organism

Saccharomyces cerevisiae S288C

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.1 %, Completeness (bb): 99.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.1 % (2197 of 2285)	97.6 % (1167 of 1196)	94.0 % (828 of 881)	97.1 % (202 of 208)
Backbone	99.6 % (1112 of 1116)	99.7 % (381 of 382)	99.6 % (550 of 552)	99.5 % (181 of 182)
Sidechain	93.8 % (1261 of 1345)	96.6 % (786 of 814)	89.9 % (454 of 505)	80.8 % (21 of 26)
Aromatic	69.2 % (126 of 182)	86.8 % (79 of 91)	50.0 % (44 of 88)	100.0 % (3 of 3)
Methyl	100.0 % (180 of 180)	100.0 % (90 of 90)	100.0 % (90 of 90)

1. entity 1

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 1 mM [U-13C; U-15N] Box C/D snoRNA protein 1, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 1 mM [U-13C; U-15N; U-2H] Box C/D snoRNA protein 1, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	Box C/D snoRNA protein 1	[U-13C; U-15N; U-2H]	1 mM
6	sodium chloride	natural abundance	150 mM
7	sodium phosphate	natural abundance	10 mM
8	TCEP	natural abundance	0.5 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 1 mM [U-15N] Box C/D snoRNA protein 1, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 12 mg/mL Pf1 phage, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	Box C/D snoRNA protein 1	[U-15N]	1 mM
10	sodium chloride	natural abundance	150 mM
11	sodium phosphate	natural abundance	10 mM
12	TCEP	natural abundance	0.5 mM
13	Pf1 phage	natural abundance	12 mg/mL

Protein Blocks Logo

Calculated from 20 models in PDB: 6NZ2, Strand ID: A Detail

Release date

2019-02-20

Citation

The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity
Bragantini, B., Charron, C., Bourguet, M., Paul, A., Tiotiu, D., Rothe, B., Marty, H., Terral, G., Hessmann, S., Decourty, L., Chagot, M.E., Strub, J.M., Massenet, S., Bertrand, E., Quinternet, M., Saveanu, C., Cianferani, S., Labialle, S., Manival, X., Charpentier, B.
Nat. Commun. (2021), 12, 1859-1859, PubMed 33767140 , DOI 10.1038/s41467-021-22077-4 , Abstract

Related entities 1. Box C/D snoRNA protein 1, : 1 : 3 : 5 entities Detail

Interaction partners 1. Box C/D snoRNA protein 1, : 14 interactors Detail

More details for 14 interactors identified by 2 citations

Experiments performed 26 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 1 mM [U-13C; U-15N] Box C/D snoRNA protein 1, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

4 3D HNCA

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

5 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

6 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

7 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 1 mM [U-13C; U-15N; U-2H] Box C/D snoRNA protein 1, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	Box C/D snoRNA protein 1	[U-13C; U-15N; U-2H]	1 mM
6	sodium chloride	natural abundance	150 mM
7	sodium phosphate	natural abundance	10 mM
8	TCEP	natural abundance	0.5 mM

8 3D CCCONH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
5	Box C/D snoRNA protein 1	[U-13C; U-15N; U-2H]	1 mM
6	sodium chloride	natural abundance	150 mM
7	sodium phosphate	natural abundance	10 mM
8	TCEP	natural abundance	0.5 mM

9 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
5	Box C/D snoRNA protein 1	[U-13C; U-15N; U-2H]	1 mM
6	sodium chloride	natural abundance	150 mM
7	sodium phosphate	natural abundance	10 mM
8	TCEP	natural abundance	0.5 mM

10 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

11 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

13 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

14 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

15 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 950 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

16 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

17 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

18 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

19 3D HNHA

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

20 3D HCCH-COSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Box C/D snoRNA protein 1	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	10 mM
4	TCEP	natural abundance	0.5 mM

21 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
5	Box C/D snoRNA protein 1	[U-13C; U-15N; U-2H]	1 mM
6	sodium chloride	natural abundance	150 mM
7	sodium phosphate	natural abundance	10 mM
8	TCEP	natural abundance	0.5 mM

22 3D HNCACO

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
5	Box C/D snoRNA protein 1	[U-13C; U-15N; U-2H]	1 mM
6	sodium chloride	natural abundance	150 mM
7	sodium phosphate	natural abundance	10 mM
8	TCEP	natural abundance	0.5 mM

23 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
5	Box C/D snoRNA protein 1	[U-13C; U-15N; U-2H]	1 mM
6	sodium chloride	natural abundance	150 mM
7	sodium phosphate	natural abundance	10 mM
8	TCEP	natural abundance	0.5 mM

24 3D HNCA

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
5	Box C/D snoRNA protein 1	[U-13C; U-15N; U-2H]	1 mM
6	sodium chloride	natural abundance	150 mM
7	sodium phosphate	natural abundance	10 mM
8	TCEP	natural abundance	0.5 mM

25 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
5	Box C/D snoRNA protein 1	[U-13C; U-15N; U-2H]	1 mM
6	sodium chloride	natural abundance	150 mM
7	sodium phosphate	natural abundance	10 mM
8	TCEP	natural abundance	0.5 mM

26 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.4, Details 1 mM [U-15N] Box C/D snoRNA protein 1, 150 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM TCEP, 12 mg/mL Pf1 phage, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	Box C/D snoRNA protein 1	[U-15N]	1 mM
10	sodium chloride	natural abundance	150 mM
11	sodium phosphate	natural abundance	10 mM
12	TCEP	natural abundance	0.5 mM
13	Pf1 phage	natural abundance	12 mg/mL

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30570_3.str
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

Content subtype: bmr30570_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	2381		99.5 (chain: 1, length: 188)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 188, Sequence coverage: 99.5%
- Total number of assignments
  - ¹H chemical shifts: 1355
  - ¹³C chemical shifts: 824
  - ¹⁵N chemical shifts: 202
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
94	TYR	HH	7.701
122	SER	HG	5.652
161	THR	HG1	5.792
168	THR	HG1	5.747

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1196	1159	96.9
¹³C chemical shifts	881	824	93.5
¹⁵N chemical shifts	208	202	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	382	378	99.0
¹³C chemical shifts	376	373	99.2
¹⁵N chemical shifts	182	181	99.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	814	781	95.9
¹³C chemical shifts	505	451	89.3
¹⁵N chemical shifts	26	21	80.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	96	98.0
¹³C chemical shifts	98	96	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	91	77	84.6
¹³C chemical shifts	88	42	47.7
¹⁵N chemical shifts	3	3	100.0

Keywords RNA BINDING PROTEIN, RNA binding, snoRNP assembly

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Found 1 Document (0.827 seconds)

BMRB: 30570

Sample #1

Sample #2

Sample #3

Related entities 1. Box C/D snoRNA protein 1, : 1 : 3 : 5 entities Detail

Interaction partners 1. Box C/D snoRNA protein 1, : 14 interactors Detail

Experiments performed 26 experiments Detail

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