BMRBj - BMREntryMaster

Found 1 Document (0.27 seconds)

BMRB: 34838

Short RNA binding to peptide amyloids

Authors

Rout, S.K., Cadalbert, R., Schroder, N., Wiegand, T., Zehnder, J., Gampp, O., Guntert, P., Kringler, D., Kreutz, C., Knorlein, A., Hall, J., Greenwald, J., Riek, R.

Assembly

VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE/RNA Complex

Entity

1. VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE/RNA Complex, entity 1 (polymer, Thiol state: not present), 9 monomers, 853.9848 × 10 Da Detail

VAQAQINIX

2. VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE/RNA Complex, entity 2 (polymer, Thiol state: not present), 4 monomers, 1303.774 Da Detail

GUCA

Total weight

9843.622 Da

Max. entity weight

1303.774 Da

Source organism

Escherichia coli

Exptl. method

solid-state NMR

Data set

assigned_chemical_shifts

Chemcal Shifts

¹³C: 39 assignments Detail

ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err	Ambig. code
1	1	1	VAL	C	C	170.446	0.400	1
2	1	1	VAL	CA	C	60.444	0.400	1
3	1	1	VAL	CB	C	32.677	0.400	1
4	1	1	VAL	CG1	C	19.694	0.400	1
5	1	1	VAL	CG2	C	18.468	0.400	1
6	1	2	ALA	C	C	173.598	0.400	1
7	1	2	ALA	CA	C	49.184	0.400	1
8	1	2	ALA	CB	C	22.888	0.400	1
9	1	3	GLN	C	C	173.164	0.400	1
10	1	3	GLN	CA	C	53.450	0.400	1
11	1	3	GLN	CB	C	31.700	0.400	1
12	1	3	GLN	CG	C	32.361	0.400	1
13	1	4	ALA	C	C	174.689	0.400	1
14	1	4	ALA	CA	C	48.875	0.400	1
15	1	4	ALA	CB	C	23.422	0.400	1
16	1	5	GLN	C	C	174.186	0.400	1
17	1	5	GLN	CA	C	53.706	0.400	1
18	1	5	GLN	CB	C	31.380	0.400	1
19	1	5	GLN	CG	C	31.342	0.400	1
20	1	6	ILE	C	C	173.973	0.400	1
21	1	6	ILE	CA	C	59.450	0.400	1
22	1	6	ILE	CB	C	41.632	0.400	1
23	1	6	ILE	CG1	C	28.037	0.400	1
24	1	6	ILE	CG2	C	16.038	0.400	1
25	1	6	ILE	CD1	C	14.485	0.400	1
26	1	7	ASN	C	C	172.203	0.400	1
27	1	7	ASN	CA	C	52.243	0.400	1
28	1	7	ASN	CB	C	41.200	0.400	1
29	1	8	ILE	C	C	176.413	0.400	1
30	1	8	ILE	CA	C	58.711	0.400	1
31	1	8	ILE	CB	C	40.250	0.400	1
32	1	8	ILE	CG1	C	26.607	0.400	1
33	1	8	ILE	CG2	C	17.885	0.400	1
34	1	8	ILE	CD1	C	13.250	0.400	1
35	2	1	G	C8	C	131.001	0.400	1
36	2	2	U	C6	C	143.857	0.400	1
37	2	3	C	C6	C	138.397	0.400	1
38	2	4	A	C2	C	152.027	0.400	1
39	2	4	A	C8	C	142.084	0.400	1

Release date

2023-11-04

Citation

An Analysis of Nucleotide-Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA
Rout, S.K., Cadalbert, R., Schroder, N., Wang, J., Zehnder, J., Gampp, O., Wiegand, T., Guntert, P., Klingler, D., Kreutz, C., Knorlein, A., Hall, J., Greenwald, J., Riek, R.
J. Am. Chem. Soc. (2023), 145, 21915-21924, PubMed 37782045 , DOI 10.1021/jacs.3c06287 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 52049 released on 2023-07-19
Title An analysis of nucleotide-amyloid interactions reveals selective binding to codon-sized RNA

Experiments performed 20 experiments Detail

1 DARR 20 ms

Instrument

Bruker AVANCE III - 850 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 272 K, pH 3, Details 10 na [U-13C; U-15N] VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE, 1.5 na [U-13C; U-15N] RNA (5'-R(P*GP*UP*CP*A)-3'), 100% D2O

#	Name	Isotope labeling	Type	Concentration
1	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
2	RNA (5'-R(PGPUPCPA)-3')	[U-13C; U-15N]		1.5 na

2 DARR 150 ms

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
2	RNA (5'-R(PGPUPCPA)-3')	[U-13C; U-15N]		1.5 na

3 NCA

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
2	RNA (5'-R(PGPUPCPA)-3')	[U-13C; U-15N]		1.5 na

4 NCO

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
2	RNA (5'-R(PGPUPCPA)-3')	[U-13C; U-15N]		1.5 na

5 DARR 20 ms

Instrument

Bruker AVANCE III - 850 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 272 K, pH 3, Details 10 na mixed VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE, 1.5 na [U-13C; U-15N] RNA (5'-R(P*GP*UP*CP*A)-3'), 100% D2O

#	Name	Isotope labeling	Type	Concentration
3	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	mixed		10 na
4	RNA (5'-R(PGPUPCPA)-3')	[U-13C; U-15N]		1.5 na

6 CHHP

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
8	RNA (5'-R(PGPUPCPA)-3')	natural abundance		1.5 na

7 PAIN 6 ms

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
5	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	mixed		10 na
6	RNA (5'-R(PGPUPCPA)-3')	[U-13C; U-15N]		1.5 na

8 CHHC

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	mixed		10 na
4	RNA (5'-R(PGPUPCPA)-3')	[U-13C; U-15N]		1.5 na

9 CHHC

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
2	RNA (5'-R(PGPUPCPA)-3')	[U-13C; U-15N]		1.5 na

10 DARR 450 ms

Instrument

Bruker AVANCE III - 850 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 272 K, pH 3, Details 10 na [U-13C; U-15N] VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE, 1.5 na specificly labeled RNA (5'-R(P*GP*UP*CP*A)-3'), 100% D2O

#	Name	Isotope labeling	Type	Concentration
9	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
10	RNA (5'-R(PGPUPCPA)-3')	specificly labeled		1.5 na

11 DARR 150 ms

Instrument

Bruker AVANCE III - 850 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 272 K, pH 3, Details 10 na [U-13C; U-15N] VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE, 1.5 na specificly labeled RNA (5'-R(P*GP*UP*CP*A)-3'), 100% D2O

#	Name	Isotope labeling	Type	Concentration
9	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
10	RNA (5'-R(PGPUPCPA)-3')	specificly labeled		1.5 na

12 NCO

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
8	RNA (5'-R(PGPUPCPA)-3')	natural abundance		1.5 na

13 NCA

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
8	RNA (5'-R(PGPUPCPA)-3')	natural abundance		1.5 na

14 DARR 20 ms

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
8	RNA (5'-R(PGPUPCPA)-3')	natural abundance		1.5 na

15 DARR 20 ms

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
5	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	mixed		10 na
6	RNA (5'-R(PGPUPCPA)-3')	[U-13C; U-15N]		1.5 na

16 PDSD

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
5	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	mixed		10 na
6	RNA (5'-R(PGPUPCPA)-3')	[U-13C; U-15N]		1.5 na

17 PAR 8 ms

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
5	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	mixed		10 na
6	RNA (5'-R(PGPUPCPA)-3')	[U-13C; U-15N]		1.5 na

18 DARR 150 ms

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	mixed		10 na
4	RNA (5'-R(PGPUPCPA)-3')	[U-13C; U-15N]		1.5 na

19 31P DP

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
8	RNA (5'-R(PGPUPCPA)-3')	natural abundance		1.5 na

20 31P PDSD

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	VAL-ALA-GLN-ALA-GLN-ILE-ASN-ILE	[U-13C; U-15N]		10 na
8	RNA (5'-R(PGPUPCPA)-3')	natural abundance		1.5 na

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34838_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	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr34838_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	39		100.0 (chain: 2, length: 4), 88.9 (chain: 1, length: 9)
1	Chemical shift references	chem_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 2, Chain length: 4, Sequence coverage: 100.0%
  - Entity_assembly_ID: 1, Chain length: 9, Sequence coverage: 88.9%
- Total number of assignments
  - ¹³C chemical shifts: 39
- Completeness of assignments
  - Entity_assemble_ID: 2
  - Entity_assemble_ID: 1
- 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 (%)
¹³C chemical shifts	27	5	18.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	20	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	7	5	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	3	3	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	34	34	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	18	18	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	8	8	100.0

Keywords RNA, UNKNOWN FUNCTION, amyloids, genetic code, origin of life

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 (0.27 seconds)

BMRB: 34838

Entries sharing articles BMRB: 1 entries Detail

Experiments performed 20 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 4 contents Detail