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Found 1 Document (0.855 seconds)

BMRB: 17574

2LBS

Structure of a yeast RNase III dsRBD complex with a non-canonical RNA substrate provides new insights into substrate recognition

Authors

Wang, Z., Hartman, E., Roy, K., Chanfreau, G., Feigon, J.

Assembly

yeast RNase III dsRBD complex with a non-canonical RNA substrate

Entity

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

GSLDMNAKRQ LYSLIGYASL RLHYVTVKKP TAVDPNSIVE CRVGDGTVLG TGVGRNIKIA GIRAAENALR DKKMLDFYAK QRAAIPRSES

2. non-canonical RNA substrate (polymer, Thiol state: not present), 32 monomers, 10345.09 Da Detail

GGGAUACCAU GUUCAAGUGA ACGUGGUAUC UC

Total weight

20151.324 Da

Max. entity weight

10345.09 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 72.1 %, Completeness: 55.7 %, Completeness (bb): 57.1 % Detail

Polymer type: polypeptide(L) DNA/RNA hybrid

	Total	¹H	¹³C	¹⁵N
All	55.7 % (854 of 1533)	54.4 % (441 of 810)	53.3 % (326 of 612)	78.4 % (87 of 111)
Backbone	57.1 % (506 of 886)	46.7 % (176 of 377)	58.8 % (248 of 422)	94.3 % (82 of 87)
Sidechain	58.8 % (429 of 729)	61.2 % (265 of 433)	58.5 % (159 of 272)	20.8 % (5 of 24)
Aromatic	8.9 % (17 of 192)	17.7 % (17 of 96)	0.0 % (0 of 78)	0.0 % (0 of 18)
Methyl	92.9 % (104 of 112)	94.6 % (53 of 56)	91.1 % (51 of 56)

1. yeast RNase III dsRBD

GSLDMNAKRQ LYSLIGYASL RLHYVTVKKP TAVDPNSIVE CRVGDGTVLG TGVGRNIKIA GIRAAENALR DKKMLDFYAK QRAAIPRSES

2. non-canonical RNA substrate

GGGAUACCAU GUUCAAGUGA ACGUGGUAUC UC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
2	entity_2	natural abundance	1.0 ~ 2.0 mM
3	NaCl	natural abundance	150 mM
4	phosphate buffer	natural abundance	20 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	entity_1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
6	entity_2	natural abundance	1.0 ~ 2.0 mM
7	NaCl	natural abundance	150 mM
8	phosphate buffer	natural abundance	20 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	entity_1	natural abundance	0.8 ~ 1.0 mM
10	entity_2	[U-100% 13C; U-100% 15N]	1.0 ~ 2.0 mM
11	NaCl	natural abundance	150 mM
12	phosphate buffer	natural abundance	20 mM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	entity_1	natural abundance	0.8 ~ 1.0 mM
14	entity_2	[U-100% 13C; U-100% 15N]	1.0 ~ 2.0 mM
15	NaCl	natural abundance	150 mM
16	phosphate buffer	natural abundance	20 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.15 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.15 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.06 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2011-04-10

Citation 1

Structure of a yeast RNase III dsRBD complex with a non-canonical RNA substrate provides new insights into substrate recognition
Wang, Z., Hartman, E., Roy, K., Chanfreau, G., Feigon, J.
Not known

Show more 1 citaion

Citation 2

Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase III
Wu, H., Henras, A., Chanfreau, G., Feigon, J.
Proc. Natl. Acad. Sci. U. S. A. (2004), 101, 8307-8312, PubMed 15150409 , DOI 10.1073/pnas.0402627101 , Abstract

Hide non-primary 1 citaion

Related entities 1. yeast RNase III dsRBD, : 1 : 3 : 6 : 1 entities Detail

Related entities 2. non-canonical RNA substrate, : 1 : 2 : 2 entities Detail

Interaction partners 1. yeast RNase III dsRBD, : 26 interactors Detail

More details for 26 interactors identified by 10 citations

Experiments performed 12 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

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
2	entity_2	natural abundance	1.0 ~ 2.0 mM
3	NaCl	natural abundance	150 mM
4	phosphate buffer	natural abundance	20 mM

2 2D 1H-1H TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	entity_1	natural abundance	0.8 ~ 1.0 mM
14	entity_2	[U-100% 13C; U-100% 15N]	1.0 ~ 2.0 mM
15	NaCl	natural abundance	150 mM
16	phosphate buffer	natural abundance	20 mM

3 2D 1H-1H NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	entity_1	natural abundance	0.8 ~ 1.0 mM
10	entity_2	[U-100% 13C; U-100% 15N]	1.0 ~ 2.0 mM
11	NaCl	natural abundance	150 mM
12	phosphate buffer	natural abundance	20 mM

4 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
2	entity_2	natural abundance	1.0 ~ 2.0 mM
3	NaCl	natural abundance	150 mM
4	phosphate buffer	natural abundance	20 mM

5 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
2	entity_2	natural abundance	1.0 ~ 2.0 mM
3	NaCl	natural abundance	150 mM
4	phosphate buffer	natural abundance	20 mM

6 3D HCCH-TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	entity_1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
6	entity_2	natural abundance	1.0 ~ 2.0 mM
7	NaCl	natural abundance	150 mM
8	phosphate buffer	natural abundance	20 mM

7 3D HCCH-COSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	entity_1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
6	entity_2	natural abundance	1.0 ~ 2.0 mM
7	NaCl	natural abundance	150 mM
8	phosphate buffer	natural abundance	20 mM

8 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
2	entity_2	natural abundance	1.0 ~ 2.0 mM
3	NaCl	natural abundance	150 mM
4	phosphate buffer	natural abundance	20 mM

9 3D 1H-13C NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	entity_1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
6	entity_2	natural abundance	1.0 ~ 2.0 mM
7	NaCl	natural abundance	150 mM
8	phosphate buffer	natural abundance	20 mM

10 2D 1H-1H COSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	entity_1	natural abundance	0.8 ~ 1.0 mM
14	entity_2	[U-100% 13C; U-100% 15N]	1.0 ~ 2.0 mM
15	NaCl	natural abundance	150 mM
16	phosphate buffer	natural abundance	20 mM

11 2D FILTERED/EDITED NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	entity_1	natural abundance	0.8 ~ 1.0 mM
14	entity_2	[U-100% 13C; U-100% 15N]	1.0 ~ 2.0 mM
15	NaCl	natural abundance	150 mM
16	phosphate buffer	natural abundance	20 mM

12 2D 1H-15N HSQC IPAP

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
2	entity_2	natural abundance	1.0 ~ 2.0 mM
3	NaCl	natural abundance	150 mM
4	phosphate buffer	natural abundance	20 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_17574_2lbs.nef
Input source #2: Coordindates	2lbs.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--
GGGAUACCAUGUUCAAGUGAACGUGGUAUCUC
||||||||||||||||||||||||||||||||
GGGAUACCAUGUUCAAGUGAACGUGGUAUCUC

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_17574_2lbs.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	913		97.8 (chain: B, length: 90)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3392 (1)	noe	100.0 (chain: A, length: 32), 100.0 (chain: B, length: 90)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	227 (227)	.	100.0 (chain: A, length: 32)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	120 (120)	.	85.6 (chain: B, length: 90)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	83 (83)	.	92.2 (chain: B, length: 90)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 97.8%
- Total number of assignments
  - ¹H chemical shifts: 500
  - ¹³C chemical shifts: 326
  - ¹⁵N chemical shifts: 87
- Completeness of assignments
  - 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	533	441	82.7
¹³C chemical shifts	397	326	82.1
¹⁵N chemical shifts	101	87	86.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	185	176	95.1
¹³C chemical shifts	180	167	92.8
¹⁵N chemical shifts	87	82	94.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	348	265	76.1
¹³C chemical shifts	217	159	73.3
¹⁵N chemical shifts	14	5	35.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	53	91.4
¹³C chemical shifts	58	51	87.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	17	73.9
¹³C chemical shifts	23	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- 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: 3383
- Weight of restraints: 1.0 (3383)
- Potential type of restraints: square-well-parabolic (3383)
- Range of distance target values: 2.05, 4.65 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- 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
- Saveframe: CNS/XPLOR_dihedral_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 85.6%
  - Total number of restraints: 120
  - Total number of restraints per polymer type: 120
  - Weight of restraints: 1.0 (120)
  - Potential type of restraints: square-well-parabolic (120)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 90, Sequence coverage: 92.2%
- Total number of restraints: 83
- Potential type of restraints: square-well-parabolic (83)
- Range of observed RDC values: -27.24, 15.87 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: B
    None

Keywords AAGU tetraloop, NMR, Rnt1p, dsRBD, solution structure

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Found 1 Document (0.855 seconds)

BMRB: 17574

Sample #1

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Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. yeast RNase III dsRBD, : 1 : 3 : 6 : 1 entities Detail

Related entities 2. non-canonical RNA substrate, : 1 : 2 : 2 entities Detail

Interaction partners 1. yeast RNase III dsRBD, : 26 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 6 contents Detail