BMRBj - BMREntryMaster

Found 1 Document (0.739 seconds)

BMRB: 34493

6Y6M

solution structure of cold-shock domain 1 and 2 of drosophila Upstream of N-Ras (Unr)

Authors

Simon, B., Hollmann, N.M., Hennig, J.

Assembly

Upstream of N-ras, isoform A

Entity

1. Upstream of N-ras, isoform A (polymer), 165 monomers, 18472.30 Da Detail

GADDEERETG IIEKLLHSYG FIQCCERQAR LFFHFSQFSG NIDHLKIGDP VEFEMTYDRR TGKPIASQVS KIAPEVVLSE ERVTGTVTTE LRTDSANNVL NSSETTGRIS YENRGECFFL PYTKDDVEGN VNLRAGDKVS FQIATNQRGN LGACHIRLEN PAQPV

Formula weight

18472.3 Da

Source organism

Drosophila melanogaster

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.4 %, Completeness: 79.8 %, Completeness (bb): 82.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.8 % (1511 of 1893)	83.4 % (816 of 978)	72.1 % (524 of 727)	91.0 % (171 of 188)
Backbone	82.2 % (804 of 978)	95.8 % (323 of 337)	67.2 % (324 of 482)	98.7 % (157 of 159)
Sidechain	80.1 % (855 of 1067)	76.8 % (492 of 641)	87.9 % (349 of 397)	48.3 % (14 of 29)
Aromatic	44.9 % (62 of 138)	52.2 % (36 of 69)	37.7 % (26 of 69)
Methyl	98.2 % (167 of 170)	96.5 % (82 of 85)	100.0 % (85 of 85)

1. entity 1

GADDEERETG IIEKLLHSYG FIQCCERQAR LFFHFSQFSG NIDHLKIGDP VEFEMTYDRR TGKPIASQVS KIAPEVVLSE ERVTGTVTTE LRTDSANNVL NSSETTGRIS YENRGECFFL PYTKDDVEGN VNLRAGDKVS FQIATNQRGN LGACHIRLEN PAQPV

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 50 mM sodium chloride, 20 mM sodium phosphate, 10 mM DTT, 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.36 mM RNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	protein	[U-99% 13C; U-99% 15N]	0.3 mM
5	RNA	natural abundance	0.36 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 50 mM sodium chloride, 20 mM sodium phosphate, 10 mM DTT, 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.36 mM RNA, 100% D2O

#	Name	Isotope labeling	Concentration
6	sodium chloride	natural abundance	50 mM
7	sodium phosphate	natural abundance	20 mM
8	DTT	natural abundance	10 mM
9	protein	[U-99% 13C; U-99% 15N]	0.3 mM
10	RNA	natural abundance	0.36 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6Y6M, Strand ID: A Detail

Release date

2020-07-12

Citation

Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras
Hollmann, N.M., Jagtap, P.K.A., Masiewicz, P., Guitart, T., Simon, B., Provaznik, J., Stein, F., Haberkant, P., Sweetapple, L.J., Villacorte, L., Mooijman, D., Benes, V., Savitski, M., Gebauer, F., Hennig, J.
Cell Rep. (2020), 32, 107930-107930, PubMed 32697992 , DOI 10.1016/j.celrep.2020.107930 , Abstract

Related entities 1. Upstream of N-ras, isoform A, : 1 : 1 : 35 entities Detail

Experiments performed 11 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 50 mM sodium chloride, 20 mM sodium phosphate, 10 mM DTT, 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.36 mM RNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	protein	[U-99% 13C; U-99% 15N]	0.3 mM
5	RNA	natural abundance	0.36 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 50 mM sodium chloride, 20 mM sodium phosphate, 10 mM DTT, 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.36 mM RNA, 100% D2O

#	Name	Isotope labeling	Concentration
6	sodium chloride	natural abundance	50 mM
7	sodium phosphate	natural abundance	20 mM
8	DTT	natural abundance	10 mM
9	protein	[U-99% 13C; U-99% 15N]	0.3 mM
10	RNA	natural abundance	0.36 mM

3 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	protein	[U-99% 13C; U-99% 15N]	0.3 mM
5	RNA	natural abundance	0.36 mM

4 3D HNCA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	protein	[U-99% 13C; U-99% 15N]	0.3 mM
5	RNA	natural abundance	0.36 mM

5 3D HNCACB

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	protein	[U-99% 13C; U-99% 15N]	0.3 mM
5	RNA	natural abundance	0.36 mM

6 3D HCCH-TOCSY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	sodium chloride	natural abundance	50 mM
7	sodium phosphate	natural abundance	20 mM
8	DTT	natural abundance	10 mM
9	protein	[U-99% 13C; U-99% 15N]	0.3 mM
10	RNA	natural abundance	0.36 mM

7 3D HBHA(CO)NH

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	protein	[U-99% 13C; U-99% 15N]	0.3 mM
5	RNA	natural abundance	0.36 mM

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	sodium chloride	natural abundance	50 mM
7	sodium phosphate	natural abundance	20 mM
8	DTT	natural abundance	10 mM
9	protein	[U-99% 13C; U-99% 15N]	0.3 mM
10	RNA	natural abundance	0.36 mM

9 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	protein	[U-99% 13C; U-99% 15N]	0.3 mM
5	RNA	natural abundance	0.36 mM

10 3D HN(CO)CA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	50 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	protein	[U-99% 13C; U-99% 15N]	0.3 mM
5	RNA	natural abundance	0.36 mM

11 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	sodium chloride	natural abundance	50 mM
7	sodium phosphate	natural abundance	20 mM
8	DTT	natural abundance	10 mM
9	protein	[U-99% 13C; U-99% 15N]	0.3 mM
10	RNA	natural abundance	0.36 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34493_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: bmr34493_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1702		99.4 (chain: 1, length: 165)
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: 165, Sequence coverage: 99.4%
- Total number of assignments
  - ¹H chemical shifts: 1016
  - ¹³C chemical shifts: 518
  - ¹⁵N chemical shifts: 168
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	978	844	86.3
¹³C chemical shifts	727	518	71.3
¹⁵N chemical shifts	188	168	89.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	337	330	97.9
¹³C chemical shifts	330	164	49.7
¹⁵N chemical shifts	159	154	96.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	641	514	80.2
¹³C chemical shifts	397	354	89.2
¹⁵N chemical shifts	29	14	48.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	86	86	100.0
¹³C chemical shifts	86	86	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	36	52.2
¹³C chemical shifts	69	26	37.7

Keywords CSD, RNA BINDING PROTEIN, ncCSD

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Found 1 Document (0.739 seconds)

BMRB: 34493

Sample #1

Sample #2

Related entities 1. Upstream of N-ras, isoform A, : 1 : 1 : 35 entities Detail

Experiments performed 11 experiments Detail

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Chemical shift validation 3 contents Detail