BMRBj - BMREntryMaster

Found 1 Document (0.663 seconds)

BMRB: 25867

2N8V

An NMR/SAXS structure of the PKI domain of the honeybee dicistrovirus, Israeli acute paralysis virus (IAPV) IRES

Authors

Au, H.H., Cornilescu, G., Mouzakis, K.D., Burke, J.E., Ren, Q., Lee, S., Butcher, S.E., Jan, E.

Assembly

PKI domain of the honeybee dicistrovirus, Israeli acute paralysis virus (IAPV) IRES

Entity

1. PKI domain of the honeybee dicistrovirus, Israeli acute paralysis virus (IAPV) IRES (polymer, Thiol state: not present), 70 monomers, 22628.41 Da Detail

GGAACAGCUG UACUGGGCAG UUACAGCAGU CGUAUGGUAA CACAUGCGGC GUUCCGAAAU ACCAUGCCUG

Formula weight

22628.41 Da

Source organism

Apis mellifera

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 41.4 %, Completeness: 9.0 %, Completeness (bb): 0.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹⁵N
All	9.0 % (58 of 644)	4.8 % (29 of 609)	82.9 % (29 of 35)
Suger, PO4	0.0 % (0 of 420)	0.0 % (0 of 420)
Nucleobase	25.9 % (58 of 224)	15.3 % (29 of 189)	82.9 % (29 of 35)
Aromatic	30.5 % (58 of 190)	18.7 % (29 of 155)	82.9 % (29 of 35)

1. RNA (70-MER)

GGAACAGCUG UACUGGGCAG UUACAGCAGU CGUAUGGUAA CACAUGCGGC GUUCCGAAAU ACCAUGCCUG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3, Details 0.53-0.70 mM; potassium phosphate 10 mM; potassium chloride 200 mM; Ethylenediaminetetraacetic acid 50 uM

#	Name	Isotope labeling	Concentration
1	RNA (70-MER)	[U-13C; U-15N]-Gua	0.53 ~ 0.7 (±0.02) mM
2	potassium phosphate	natural abundance	10 mM
3	potassium chloride	natural abundance	200 mM
4	Ethylenediaminetetraacetic acid	natural abundance	50 uM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3, Details Pf1 phage 12.5 mg/mL 0.53-0.70 mM; potassium phosphate 10 mM; potassium chloride 200 mM; Ethylenediaminetetraacetic acid 50 uM

#	Name	Isotope labeling	Concentration
7	RNA (70-MER)	[U-13C; U-15N]-Gua	0.53 ~ 0.7 (±0.02) mM
8	Pf1 phage	natural abundance	12.5 mg/mL
9	potassium phosphate	natural abundance	10 mM
10	potassium chloride	natural abundance	200 mM
11	Ethylenediaminetetraacetic acid	natural abundance	50 uM
12	H2O	natural abundance	90 %
13	D2O	natural abundance	10 %

Release date

2015-11-08

Citation

Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection
Au, H.H., Cornilescu, G., Mouzakis, K.D., Ren, Q., Burke, J.E., Lee, S., Butcher, S.E., Jan, E.
Proc. Natl. Acad. Sci. U. S. A. (2015), 112, E6446-E6455, PubMed 26554019 , DOI 10.1073/pnas.1512088112 , Abstract

Experiments performed 2 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, RDC restraints	combined_25867_2n8v.nef
Input source #2: Coordindates	2n8v.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): X vs Auth_asym_ID (model): X

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
X	X	70	0	0	100.0

Content subtype: combined_25867_2n8v.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	58		41.4 (chain: X, length: 70)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	36 (1)	noe	52.9 (chain: X, length: 70)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	28 (28)	.	40.0 (chain: X, length: 70)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: X, Chain length: 70, Sequence coverage: 41.4%
- Total number of assignments
  - ¹H chemical shifts: 29
  - ¹⁵N chemical shifts: 29
- Completeness of assignments
- Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: X, Chain length: 70, Sequence coverage: 52.9%
- Total number of restraints: 36
- Weight of restraints: 1.0 (36)
- Potential type of restraints: square-well-parabolic (36)
- Range of distance target values: 2.25, 4.1 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: X
- Distance restraints on contact map

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: X, Chain length: 70, Sequence coverage: 40.0%
- Total number of restraints: 28
- Potential type of restraints: square-well-parabolic (28)
- Range of observed RDC values: -34.4, 31.2 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue

Keywords IAPV, RNA, pseudoknot

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 (0.663 seconds)

BMRB: 25867

Sample #1

Sample #2

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail