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Found 1 Document (0.777 seconds)

BMRB: 18534

2LUP

RDC REFINED SOLUTION STRUCTURE OF DOUBLE-STRANDED RNA BINDING DOMAIN OF S. CEREVISIAE RNASE III (RNT1P) IN COMPLEX WITH THE TERMINAL RNA HAIRPIN OF SNR47 PRECURSOR

Authors

Wang, Z., Feigon, J.

Assembly

Ribonuclease III in complex with RNA (32-MER)

Entity

1. Ribonuclease III (polymer, Thiol state: all free), 90 monomers, 9806.233 Da Detail

GSLDMNAKRQ LYSLIGYASL RLHYVTVKKP TAVDPNSIVE CRVGDGTVLG TGVGRNIKIA GIRAAENALR DKKMLDFYAK QRAAIPRSES

2. RNA (32-MER) (polymer, Thiol state: not present), 32 monomers, 10368.13 Da Detail

GGGAUACCAU GUUCAGAAGA ACGUGGUAUC UC

Total weight

20174.363 Da

Max. entity weight

10368.13 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 82.8 %, Completeness (bb): 90.6 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	82.8 % (1268 of 1531)	83.3 % (674 of 809)	82.2 % (503 of 612)	82.7 % (91 of 110)
Backbone	90.6 % (803 of 886)	98.4 % (371 of 377)	82.2 % (347 of 422)	97.7 % (85 of 87)
Sidechain	75.2 % (547 of 727)	70.1 % (303 of 432)	87.5 % (238 of 272)	26.1 % (6 of 23)
Aromatic	70.0 % (133 of 190)	82.1 % (78 of 95)	70.5 % (55 of 78)	0.0 % (0 of 17)
Methyl	77.7 % (87 of 112)	60.7 % (34 of 56)	94.6 % (53 of 56)

1. Ribonuclease III

GSLDMNAKRQ LYSLIGYASL RLHYVTVKKP TAVDPNSIVE CRVGDGTVLG TGVGRNIKIA GIRAAENALR DKKMLDFYAK QRAAIPRSES

2. RNA (32-MER)

GGGAUACCAU GUUCAGAAGA ACGUGGUAUC UC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
1	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	sodium phosphate	natural abundance	20 mM
5	sodium chloride	natural abundance	150 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
6	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	10 mM
9	sodium phosphate	natural abundance	150 mM

Protein Blocks Logo

Calculated from 16 models in PDB: 2LUP, Strand ID: B Detail

Release date

2013-02-19

Citation

Structure of a yeast RNase III dsRBD complex with a noncanonical RNA substrate provides new insights into binding specificity of dsRBDs
Wang, Z., Hartman, E., Roy, K., Chanfreau, G., Feigon, J.
Structure (2011), 19, 999-1010, PubMed 21742266 , DOI 10.1016/j.str.2011.03.022 , Abstract

Related entities 1. Ribonuclease III, : 1 : 3 : 6 : 1 entities Detail

Related entities 2. RNA (32-MER), : 1 : 1 : 1 entities Detail

Interaction partners 1. Ribonuclease III, : 26 interactors Detail

More details for 26 interactors identified by 10 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
1	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	sodium phosphate	natural abundance	20 mM
5	sodium chloride	natural abundance	150 mM

2 3D HNCACB

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
1	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	sodium phosphate	natural abundance	20 mM
5	sodium chloride	natural abundance	150 mM

3 3D HBHA(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
1	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	sodium phosphate	natural abundance	20 mM
5	sodium chloride	natural abundance	150 mM

4 3D HNCO

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
1	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	sodium phosphate	natural abundance	20 mM
5	sodium chloride	natural abundance	150 mM

5 3D HCCH-TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
6	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	10 mM
9	sodium phosphate	natural abundance	150 mM

6 3D HCCH-COSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
6	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	10 mM
9	sodium phosphate	natural abundance	150 mM

7 3D 1H-15N NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
1	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	sodium phosphate	natural abundance	20 mM
5	sodium chloride	natural abundance	150 mM

8 3D 1H-13C NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
6	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	10 mM
9	sodium phosphate	natural abundance	150 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18534_2lup.nef
Input source #2: Coordindates	2lup.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

--------10--------20--------30--
GGGAUACCAUGUUCAGAAGAACGUGGUAUCUC
||||||||||||||||||||||||||||||||
GGGAUACCAUGUUCAGAAGAACGUGGUAUCUC

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

----370-------380-------390-------400-------410-------420-------430-------440-------450---
GSLDMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDFYAKQRAAIPRSES
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSLDMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDFYAKQRAAIPRSES
--------10--------20--------30--------40--------50--------60--------70--------80--------90

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	32	0	0	100.0
B	B	90	0	0	100.0

Content subtype: combined_18534_2lup.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1249		100.0 (chain: A, length: 32), 100.0 (chain: B, length: 90)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	2960 (1)	noe	100.0 (chain: A, length: 32), 100.0 (chain: B, length: 90)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	102 (1)	noe	48.9 (chain: B, length: 90)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	227 (227)	.	100.0 (chain: A, length: 32)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	81 (81)	.	90.0 (chain: B, length: 90)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 672
  - ¹³C chemical shifts: 487
  - ¹⁵N chemical shifts: 90
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Redox state of CYS
- Peptide bond of PRO
- 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: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	276	263	95.3
¹³C chemical shifts	215	215	100.0
¹⁵N chemical shifts	17	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	192	192	100.0
¹³C chemical shifts	160	160	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	71	84.5
¹³C chemical shifts	55	55	100.0
¹⁵N chemical shifts	17	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	27	100.0
¹³C chemical shifts	27	27	100.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
386	HIS	HD1	6.65

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	533	408	76.5
¹³C chemical shifts	397	272	68.5
¹⁵N chemical shifts	101	90	89.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	185	180	97.3
¹³C chemical shifts	180	89	49.4
¹⁵N chemical shifts	87	84	96.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	348	228	65.5
¹³C chemical shifts	217	183	84.3
¹⁵N chemical shifts	14	6	42.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	34	58.6
¹³C chemical shifts	58	55	94.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	7	30.4
¹³C chemical shifts	23	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 100.0%
- Total number of restraints: 2959
- Weight of restraints: 1.0 (2959)
- Potential type of restraints: square-well-parabolic (2959)
- Range of distance target values: 2.4, 4.4 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 48.9%
  - Total number of restraints: 102
  - Weight of restraints: 1.0 (102)
  - Potential type of restraints: square-well-parabolic (102)
  - Range of distance target values: 2.4, 3.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
      None
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 100.0%
- Total number of restraints: 227
- Total number of restraints per polymer type: 227
- Weight of restraints: 1.0 (227)
- Potential type of restraints: square-well-parabolic (227)
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 90.0%
- Total number of restraints: 81
- Potential type of restraints: square-well-parabolic (81)
- Range of observed RDC values: -37.02, 22.49 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: B
    None

Keywords double strand rna binding, DSRBD, RNT1P, SNR47

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Found 1 Document (0.777 seconds)

BMRB: 18534

Sample #1

Sample #2

Related entities 1. Ribonuclease III, : 1 : 3 : 6 : 1 entities Detail

Related entities 2. RNA (32-MER), : 1 : 1 : 1 entities Detail

Interaction partners 1. Ribonuclease III, : 26 interactors Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 6 contents Detail