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BMRB: 15958

2K8Q

NMR Structure of Shq1p N-terminal domain

Authors

Godin, K.S., Varani, G.

Assembly

Shq1p

Entity

1. Shq1p (polymer, Thiol state: all free), 134 monomers, 15366.20 Da Detail

GITPRFSITQ DEEFIFLKIF ISNIRFSAVG LEIIIQENMI IFHLSPYYLR LRFPHELIDD ERSTAQYDSK DECINVKVAK LNKNEYFEDL DLPTKLLARQ GDLAGADALT ENTDAKKTQK PLIQEVETDG VSNN

Formula weight

15366.2 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 82.2 %, Completeness (bb): 81.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.2 % (1323 of 1609)	92.8 % (778 of 838)	65.4 % (411 of 628)	93.7 % (134 of 143)
Backbone	81.6 % (648 of 794)	96.6 % (259 of 268)	66.2 % (263 of 397)	97.7 % (126 of 129)
Sidechain	82.7 % (781 of 944)	89.3 % (509 of 570)	73.3 % (264 of 360)	57.1 % (8 of 14)
Aromatic	48.3 % (58 of 120)	96.7 % (58 of 60)	0.0 % (0 of 60)
Methyl	89.0 % (146 of 164)	91.5 % (75 of 82)	86.6 % (71 of 82)

1. Shq1 N-terminus

GITPRFSITQ DEEFIFLKIF ISNIRFSAVG LEIIIQENMI IFHLSPYYLR LRFPHELIDD ERSTAQYDSK DECINVKVAK LNKNEYFEDL DLPTKLLARQ GDLAGADALT ENTDAKKTQK PLIQEVETDG VSNN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 50mM KCl 50mM KPOx pH 7.0 4mM DTT

#	Name	Isotope labeling	Type	Concentration
1	Shq1 N-terminus	[U-100% 13C; U-100% 15N]		1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	KCl	natural abundance		50 mM
5	KPOx pH 7.0	natural abundance		50 mM
6	DTT	natural abundance		4 mM

LACS Plot; CA

Referencing offset: 0.21 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.21 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.07 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K8Q, Strand ID: A Detail

Release date

2009-06-01

Citation

The box H/ACA snoRNP assembly factor Shq1p is a chaperone protein homologous to Hsp90 cochaperones that binds to the Cbf5p enzyme
Godin, K.S., Walbott, H., Leulliot, N., van Tilbeurgh, H., Varani, G.
J. Mol. Biol. (2009), 390, 231-244, PubMed 19426738 , DOI 10.1016/j.jmb.2009.04.076 , Abstract

Related entities 1. Shq1p, : 1 : 2 : 15 entities Detail

Interaction partners 1. Shq1p, : 20 interactors Detail

More details for 20 interactors identified by 6 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz HNCA, HNCO, HNCOCA, CBCACONH, HAHBCONH, HNCACB

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 50mM KCl 50mM KPOx pH 7.0 4mM DTT

#	Name	Isotope labeling	Type	Concentration
1	Shq1 N-terminus	[U-100% 13C; U-100% 15N]		1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	KCl	natural abundance		50 mM
5	KPOx pH 7.0	natural abundance		50 mM
6	DTT	natural abundance		4 mM

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz HNCA, HNCO, HNCOCA, CBCACONH, HAHBCONH, HNCACB

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 50mM KCl 50mM KPOx pH 7.0 4mM DTT

#	Name	Isotope labeling	Type	Concentration
1	Shq1 N-terminus	[U-100% 13C; U-100% 15N]		1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	KCl	natural abundance		50 mM
5	KPOx pH 7.0	natural abundance		50 mM
6	DTT	natural abundance		4 mM

3 3D HNCO

Instrument

Bruker Avance - 500 MHz HNCA, HNCO, HNCOCA, CBCACONH, HAHBCONH, HNCACB

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 50mM KCl 50mM KPOx pH 7.0 4mM DTT

#	Name	Isotope labeling	Type	Concentration
1	Shq1 N-terminus	[U-100% 13C; U-100% 15N]		1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	KCl	natural abundance		50 mM
5	KPOx pH 7.0	natural abundance		50 mM
6	DTT	natural abundance		4 mM

4 3D HNCA

Instrument

Bruker Avance - 500 MHz HNCA, HNCO, HNCOCA, CBCACONH, HAHBCONH, HNCACB

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 50mM KCl 50mM KPOx pH 7.0 4mM DTT

#	Name	Isotope labeling	Type	Concentration
1	Shq1 N-terminus	[U-100% 13C; U-100% 15N]		1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	KCl	natural abundance		50 mM
5	KPOx pH 7.0	natural abundance		50 mM
6	DTT	natural abundance		4 mM

5 3D HNCACB

Instrument

Bruker Avance - 500 MHz HNCA, HNCO, HNCOCA, CBCACONH, HAHBCONH, HNCACB

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 50mM KCl 50mM KPOx pH 7.0 4mM DTT

#	Name	Isotope labeling	Type	Concentration
1	Shq1 N-terminus	[U-100% 13C; U-100% 15N]		1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	KCl	natural abundance		50 mM
5	KPOx pH 7.0	natural abundance		50 mM
6	DTT	natural abundance		4 mM

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz HNCA, HNCO, HNCOCA, CBCACONH, HAHBCONH, HNCACB

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 50mM KCl 50mM KPOx pH 7.0 4mM DTT

#	Name	Isotope labeling	Type	Concentration
1	Shq1 N-terminus	[U-100% 13C; U-100% 15N]		1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	KCl	natural abundance		50 mM
5	KPOx pH 7.0	natural abundance		50 mM
6	DTT	natural abundance		4 mM

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz HNCA, HNCO, HNCOCA, CBCACONH, HAHBCONH, HNCACB

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 50mM KCl 50mM KPOx pH 7.0 4mM DTT

#	Name	Isotope labeling	Type	Concentration
1	Shq1 N-terminus	[U-100% 13C; U-100% 15N]		1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	KCl	natural abundance		50 mM
5	KPOx pH 7.0	natural abundance		50 mM
6	DTT	natural abundance		4 mM

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 750 MHz 15N NOESY-HSQC

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 50mM KCl 50mM KPOx pH 7.0 4mM DTT

#	Name	Isotope labeling	Type	Concentration
1	Shq1 N-terminus	[U-100% 13C; U-100% 15N]		1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	KCl	natural abundance		50 mM
5	KPOx pH 7.0	natural abundance		50 mM
6	DTT	natural abundance		4 mM

9 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz 13C NOESY-HSQC

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 50mM KCl 50mM KPOx pH 7.0 4mM DTT

#	Name	Isotope labeling	Type	Concentration
1	Shq1 N-terminus	[U-100% 13C; U-100% 15N]		1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	KCl	natural abundance		50 mM
5	KPOx pH 7.0	natural abundance		50 mM
6	DTT	natural abundance		4 mM

10 2D 1H-1H NOESY

Instrument

Bruker DMX - 750 MHz 2D 1H-1H NOESY

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 50mM KCl 50mM KPOx pH 7.0 4mM DTT

#	Name	Isotope labeling	Type	Concentration
1	Shq1 N-terminus	[U-100% 13C; U-100% 15N]		1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	KCl	natural abundance		50 mM
5	KPOx pH 7.0	natural abundance		50 mM
6	DTT	natural abundance		4 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15958_2k8q.nef
Input source #2: Coordindates	2k8q.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--------40--------50--------60--------70--------80--------90-------100
GITPRFSITQDEEFIFLKIFISNIRFSAVGLEIIIQENMIIFHLSPYYLRLRFPHELIDDERSTAQYDSKDECINVKVAKLNKNEYFEDLDLPTKLLARQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GITPRFSITQDEEFIFLKIFISNIRFSAVGLEIIIQENMIIFHLSPYYLRLRFPHELIDDERSTAQYDSKDECINVKVAKLNKNEYFEDLDLPTKLLARQ

-------110-------120-------130----
GDLAGADALTENTDAKKTQKPLIQEVETDGVSNN
||||||||||||||||||||||||||||||||||
GDLAGADALTENTDAKKTQKPLIQEVETDGVSNN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	134	0	0	100.0

Content subtype: combined_15958_2k8q.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1307		100.0 (chain: A, length: 134)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3260 (1)	noe	95.5 (chain: A, length: 134)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	96 (1)	hbond	23.9 (chain: A, length: 134)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	Warning	54 (27)	.	33.6 (chain: A, length: 134)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 792
  - ¹⁵N chemical shifts: 136
  - ¹³C chemical shifts: 379
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 95.5%
- Total number of restraints: 3260
- Weight of restraints: 1.0 (3260)
- Potential type of restraints: upper-bound-parabolic (3260)
- Range of distance target values: 2.55, 5.52 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 23.9%
  - Total number of restraints: 96
  - Weight of restraints: 1.0 (96)
  - Potential type of restraints: upper-bound-parabolic (96)
  - Range of distance target values: 1.8, 3.3 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 33.6%
- Total number of restraints: 27
- Total number of restraints per polymer type: 27
- Weight of restraints: 1.0 (27)
- Potential type of restraints: square-well-parabolic (27)
- Dihedral angle restraints per residue

Keywords NMR, Shq1, box H/ACA snoRNA, CS domain, beta-sandwich