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BMRB: 25966

2NB8

Solution structure of C-terminal extramembrane domain of SH protein

Authors

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

Assembly

C-terminal extramembrane domain of SH protein

Entity

1. C-terminal extramembrane domain of SH protein (polymer, Thiol state: all free), 27 monomers, 3204.699 Da Detail

IAILNKLCEY NVFHNKTFEL PRARVNT

Formula weight

3204.699 Da

Source organism

Human orthopneumovirus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.5 %, Completeness (bb): 96.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.5 % (299 of 338)	89.8 % (158 of 176)	86.4 % (114 of 132)	90.0 % (27 of 30)
Backbone	96.2 % (154 of 160)	100.0 % (53 of 53)	92.6 % (75 of 81)	100.0 % (26 of 26)
Sidechain	83.9 % (172 of 205)	85.4 % (105 of 123)	84.6 % (66 of 78)	25.0 % (1 of 4)
Aromatic	50.0 % (16 of 32)	50.0 % (8 of 16)	50.0 % (8 of 16)
Methyl	86.1 % (31 of 36)	88.9 % (16 of 18)	83.3 % (15 of 18)

1. entity

IAILNKLCEY NVFHNKTFEL PRARVNT

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		90 %
6	D2O	[U-2H]		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2NB8, 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

Related entities 1. C-terminal extramembrane domain of SH protein, : 1 : 1 : 1 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		90 %
6	D2O	[U-2H]		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		90 %
6	D2O	[U-2H]		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		90 %
6	D2O	[U-2H]		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		90 %
6	D2O	[U-2H]		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		90 %
6	D2O	[U-2H]		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		90 %
6	D2O	[U-2H]		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		90 %
6	D2O	[U-2H]		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		90 %
6	D2O	[U-2H]		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		90 %
6	D2O	[U-2H]		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25966_2nb8.nef
Input source #2: Coordindates	2nb8.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

--40-------50--------60----
IAILNKLCEYNVFHNKTFELPRARVNT
|||||||||||||||||||||||||||
IAILNKLCEYNVFHNKTFELPRARVNT
--------10--------20-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	27	0	0	100.0

Content subtype: combined_25966_2nb8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	299		100.0 (chain: A, length: 27)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	479 (1)	noe	100.0 (chain: A, length: 27)
2	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	8 (1)	hbond	44.4 (chain: A, length: 27)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	34 (34)	.	96.3 (chain: A, length: 27)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 158
  - ¹³C chemical shifts: 112
  - ¹⁵N chemical shifts: 29
- 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_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
- Total number of restraints: 479
- Weight of restraints: 1.0 (479)
- Potential type of restraints: upper-bound-parabolic (479)
- Range of distance target values: 2.35, 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: 27, Sequence coverage: 44.4%
  - Total number of restraints: 8
  - Weight of restraints: 1.0 (8)
  - Potential type of restraints: upper-bound-parabolic (8)
  - 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: 27, Sequence coverage: 96.3%
- Total number of restraints: 34
- Total number of restraints per polymer type: 34
- Weight of restraints: 1.0 (34)
- Potential type of restraints: square-well-parabolic (34)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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