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BMRB: 25965

2NB7

Solution structure of N-terminal extramembrane domain of SH protein

Authors

Li, Y., To, J., Surya, W., Torres, J.

Assembly

N-terminal extramembrane domain of SH protein

Entity

1. N-terminal extramembrane domain of SH protein (polymer, Thiol state: not present), 14 monomers, 1633.816 Da Detail

MENTSITIEF SSKF

Formula weight

1633.816 Da

Source organism

Human orthopneumovirus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 86.4 %, Completeness (bb): 95.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.4 % (146 of 169)	86.2 % (75 of 87)	83.6 % (56 of 67)	100.0 % (15 of 15)
Backbone	95.2 % (80 of 84)	92.9 % (26 of 28)	95.2 % (40 of 42)	100.0 % (14 of 14)
Sidechain	80.8 % (80 of 99)	83.1 % (49 of 59)	76.9 % (30 of 39)	100.0 % (1 of 1)
Aromatic	30.0 % (6 of 20)	40.0 % (4 of 10)	20.0 % (2 of 10)
Methyl	100.0 % (12 of 12)	100.0 % (6 of 6)	100.0 % (6 of 6)

1. entity

MENTSITIEF SSKF

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]	protein	0.7 mM
2	DHPC-DLPC	natural abundance		9.5 %
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2NB7, Strand ID: A Detail

Release date

2016-02-14

Citation

Inhibition of the human respiratory syncytial virus small hydrophobic protein and structural variations in a bicelle environment
Li, Y., To, J., Verdia-Baguena, C., Dossena, S., Surya, W., Huang, M., Paulmichl, M., Liu, D., Aguilella, V., Torres, J.
J. Virol. (2014), 88, 11899-11914, PubMed 25100835 , DOI 10.1128/JVI.00839-14 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 25966 released on 2016-02-14
Title Solution structure of C-terminal extramembrane domain of SH protein

Related entities 1. N-terminal extramembrane domain of SH protein, : 1 : 1 : 2 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]	protein	0.7 mM
2	DHPC-DLPC	natural abundance		9.5 %
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

2 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]	protein	0.7 mM
2	DHPC-DLPC	natural abundance		9.5 %
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

3 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]	protein	0.7 mM
2	DHPC-DLPC	natural abundance		9.5 %
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]	protein	0.7 mM
2	DHPC-DLPC	natural abundance		9.5 %
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

5 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]	protein	0.7 mM
2	DHPC-DLPC	natural abundance		9.5 %
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

6 3D HN(CA)CO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]	protein	0.7 mM
2	DHPC-DLPC	natural abundance		9.5 %
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]	protein	0.7 mM
2	DHPC-DLPC	natural abundance		9.5 %
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

8 3D H(CCO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]	protein	0.7 mM
2	DHPC-DLPC	natural abundance		9.5 %
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]	protein	0.7 mM
2	DHPC-DLPC	natural abundance		9.5 %
3	sodium phosphate	natural abundance	buffer	20 mM
4	sodium chloride	natural abundance	salt	50 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25965_2nb7.nef
Input source #2: Coordindates	2nb7.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----
SNAMENTSITIEFSSKF
|||||||||||||||||
SNAMENTSITIEFSSKF
--------10-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	17	0	0	100.0

Content subtype: combined_25965_2nb7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	151		82.4 (chain: A, length: 17)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	252 (1)	noe	82.4 (chain: A, length: 17)
2	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	6 (1)	hbond	58.8 (chain: A, length: 17)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	8 (8)	.	35.3 (chain: A, length: 17)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 82.4%
- Total number of assignments
  - ¹H chemical shifts: 80
  - ¹³C chemical shifts: 56
  - ¹⁵N chemical shifts: 15
- Completeness of assignments
  - Entity_assemble_ID: A
- 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_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 82.4%
- Total number of restraints: 252
- Weight of restraints: 1.0 (252)
- Potential type of restraints: upper-bound-parabolic (252)
- Range of distance target values: 2.3, 5.5 (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_2
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 58.8%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: upper-bound-parabolic (6)
  - Range of distance target values: 2.3, 2.3 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 17, Sequence coverage: 35.3%
- Total number of restraints: 8
- Total number of restraints per polymer type: 8
- Weight of restraints: 1.0 (8)
- Potential type of restraints: square-well-parabolic (8)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords Bicelles, Human Respiratory Syncytial Virus, NMR, Small Hydrophobic Protein