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BMRB: 18655

2LX0

Arced helix (ArcH) NMR structure of the reovirus p14 fusion-associated small transmembrane (FAST) protein transmembrane domain (TMD) in dodecyl phosphocholine (DPC) micelles

Authors

Sarker, M., Key, T., Duncan, R., Rainey, J.K.

Assembly

Transmembrane Arced Helix (ArcH)

Entity

1. Transmembrane Arced Helix (ArcH) (polymer, Thiol state: not present), 32 monomers, 3810.611 Da Detail

KKHTIWEVIA GLVALLTFLA FGFWLFKYLQ KK

Formula weight

3810.611 Da

Source organism

Reptilian orthoreovirus

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 87.2 %, Completeness (bb): 70.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	87.2 % (225 of 258)	97.3 % (217 of 223)	22.9 % (8 of 35)
Backbone	70.4 % (69 of 98)	92.4 % (61 of 66)	25.0 % (8 of 32)
Sidechain	97.5 % (156 of 160)	99.4 % (156 of 157)	0.0 % (0 of 3)
Aromatic	95.0 % (38 of 40)	100.0 % (38 of 38)	0.0 % (0 of 2)
Methyl	100.0 % (25 of 25)	100.0 % (25 of 25)

1. ArcH

KKHTIWEVIA GLVALLTFLA FGFWLFKYLQ KK

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 5, Details 0.75 mM p14 TMD peptide, 150 mM deuterated dodecyl phosphocholine (DPC), 0.5 mM sodium 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 0.2 mM sodium azide, 20 mM sodium acetate, pH 5, 37 degree celcius

#	Name	Isotope labeling	Type	Concentration
1	p14 TMD peptide	Partial 15N (8 of 32 amino acids)		0.75 mM
2	DPC	[U-2H]		150 mM
3	DSS	natural abundance		0.5 mM
4	sodium azide	natural abundance		0.2 mM
5	sodium acetate	[U-2H]		20 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 50 models in PDB: 2LX0, Strand ID: A Detail

Release date

2012-09-03

Citation

A Cell-Cell Membrane Fusion Module Comprising a Transmembrane Arced Helix (ArcH)
Sarker, M., Key, T., Rainey, J.K., Duncan, R.
Not known

Related entities 1. Transmembrane Arced Helix (ArcH), : 1 : 8 entities Detail

Experiments performed 5 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz TCI 5mm probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 5, Details 0.75 mM p14 TMD peptide, 150 mM deuterated dodecyl phosphocholine (DPC), 0.5 mM sodium 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 0.2 mM sodium azide, 20 mM sodium acetate, pH 5, 37 degree celcius

#	Name	Isotope labeling	Type	Concentration
1	p14 TMD peptide	Partial 15N (8 of 32 amino acids)		0.75 mM
2	DPC	[U-2H]		150 mM
3	DSS	natural abundance		0.5 mM
4	sodium azide	natural abundance		0.2 mM
5	sodium acetate	[U-2H]		20 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz TCI 5mm probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 5, Details 0.75 mM p14 TMD peptide, 150 mM deuterated dodecyl phosphocholine (DPC), 0.5 mM sodium 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 0.2 mM sodium azide, 20 mM sodium acetate, pH 5, 37 degree celcius

#	Name	Isotope labeling	Type	Concentration
1	p14 TMD peptide	Partial 15N (8 of 32 amino acids)		0.75 mM
2	DPC	[U-2H]		150 mM
3	DSS	natural abundance		0.5 mM
4	sodium azide	natural abundance		0.2 mM
5	sodium acetate	[U-2H]		20 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz TCI 5mm probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 5, Details 0.75 mM p14 TMD peptide, 150 mM deuterated dodecyl phosphocholine (DPC), 0.5 mM sodium 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 0.2 mM sodium azide, 20 mM sodium acetate, pH 5, 37 degree celcius

#	Name	Isotope labeling	Type	Concentration
1	p14 TMD peptide	Partial 15N (8 of 32 amino acids)		0.75 mM
2	DPC	[U-2H]		150 mM
3	DSS	natural abundance		0.5 mM
4	sodium azide	natural abundance		0.2 mM
5	sodium acetate	[U-2H]		20 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

4 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz TCI 5mm probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 5, Details 0.75 mM p14 TMD peptide, 150 mM deuterated dodecyl phosphocholine (DPC), 0.5 mM sodium 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 0.2 mM sodium azide, 20 mM sodium acetate, pH 5, 37 degree celcius

#	Name	Isotope labeling	Type	Concentration
1	p14 TMD peptide	Partial 15N (8 of 32 amino acids)		0.75 mM
2	DPC	[U-2H]		150 mM
3	DSS	natural abundance		0.5 mM
4	sodium azide	natural abundance		0.2 mM
5	sodium acetate	[U-2H]		20 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz TCI 5mm probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 5, Details 0.75 mM p14 TMD peptide, 150 mM deuterated dodecyl phosphocholine (DPC), 0.5 mM sodium 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 0.2 mM sodium azide, 20 mM sodium acetate, pH 5, 37 degree celcius

#	Name	Isotope labeling	Type	Concentration
1	p14 TMD peptide	Partial 15N (8 of 32 amino acids)		0.75 mM
2	DPC	[U-2H]		150 mM
3	DSS	natural abundance		0.5 mM
4	sodium azide	natural abundance		0.2 mM
5	sodium acetate	[U-2H]		20 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18655_2lx0.nef
Input source #2: Coordindates	2lx0.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--
KKHTIWEVIAGLVALLTFLAFGFWLFKYLQKK
||||||||||||||||||||||||||||||||
KKHTIWEVIAGLVALLTFLAFGFWLFKYLQKK

Chain assignments

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

Content subtype: combined_18655_2lx0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	237		100.0 (chain: A, length: 32)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2942 (1)	noe	100.0 (chain: A, length: 32)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	660 (1)	noe	100.0 (chain: A, length: 32)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	20 (1)	hbond	40.6 (chain: A, length: 32)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	38 (38)	.	65.6 (chain: A, length: 32)

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%
- Total number of assignments
  - ¹H chemical shifts: 229
  - ¹⁵N chemical shifts: 8
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 100.0%
- Total number of restraints: 2712
- Weight of restraints: 1.0 (2712)
- Potential type of restraints: square-well-parabolic (2712)
- Range of distance target values: 2.3, 3.9 (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: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 100.0%
  - Total number of restraints: 654
  - Weight of restraints: 1.0 (654)
  - Potential type of restraints: square-well-parabolic (654)
  - Range of distance target values: 2.3, 3.9 (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: CNS/XPLOR_distance_constraints_4
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 40.6%
    - Total number of restraints: 20
    - Weight of restraints: 1.0 (20)
    - Potential type of restraints: square-well-parabolic (20)
    - Range of distance target values: 2.05, 3.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 65.6%
- Total number of restraints: 38
- Total number of restraints per polymer type: 38
- Weight of restraints: 1.0 (38)
- Potential type of restraints: square-well-parabolic (38)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ArcH, Membrane fusion protein transmembrane domain, micelle/peptide complex, NMR structure of TMD, p14 FAST protein TMD