BMRBj - BMREntryMaster

Found 1 Document (0.606 seconds)

BMRB: 25181

2MTS

Three-Dimensional Structure and Interaction Studies of Hepatitis C Virus p7 in 1,2-Dihexanoyl-sn-glycero-3-phosphocholine by Solution Nuclear Magnetic Resonance

Authors

Cook, G.A., Dawson, L.A., Tian, Y., Opella, S.J.

Assembly

Hepatitis C Virus p7

Entity

1. Hepatitis C Virus p7 (polymer, Thiol state: not present), 63 monomers, 6689.884 Da Detail

ALENLVVLNA ASVAGAHGIL SFLVFFSAAW YIKGRLAPGA AYAFYGVWPL LLLLLALPPR AYA

Formula weight

6689.884 Da

Source organism

Hepatitis C virus isolate HC-J4

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.8 %, Completeness: 28.2 %, Completeness (bb): 50.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	28.2 % (207 of 733)	20.4 % (75 of 367)	24.4 % (74 of 303)	92.1 % (58 of 63)
Backbone	50.0 % (185 of 370)	48.0 % (61 of 127)	35.9 % (66 of 184)	98.3 % (58 of 59)
Sidechain	6.2 % (26 of 421)	5.8 % (14 of 240)	6.8 % (12 of 177)	0.0 % (0 of 4)
Aromatic	0.0 % (0 of 100)	0.0 % (0 of 50)	0.0 % (0 of 48)	0.0 % (0 of 2)
Methyl	7.4 % (8 of 108)	7.4 % (4 of 54)	7.4 % (4 of 54)

1. entity

ALENLVVLNA ASVAGAHGIL SFLVFFSAAW YIKGRLAPGA AYAFYGVWPL LLLLLALPPR AYA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0

#	Name	Isotope labeling	Concentration
1	p7	[U-100% 13C; U-100% 15N]	0.5 mM
2	H2O	natural abundance	90 %
3	DHPC	natural abundance	125 mM
4	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 4.0

#	Name	Isotope labeling	Concentration
5	p7	[U-100% 15N]	0.5 mM
6	DHPC	natural abundance	125 mM
7	D2O	natural abundance	10 %
8	H2O	natural abundance	90 %
9	polyacrylamide gel	natural abundance	6 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2MTS, Strand ID: A Detail

Release date

2014-10-06

Citation

Three-dimensional structure and interaction studies of hepatitis C virus p7 in 1,2-dihexanoyl-sn-glycero-3-phosphocholine by solution nuclear magnetic resonance
Cook, G.A., Dawson, L.A., Tian, Y., Opella, S.J.
Biochemistry (2013), 52, 5295-5303, PubMed 23841474 , DOI 10.1021/bi4006623 , Abstract

Related entities 1. Hepatitis C Virus p7, : 1 : 4 : 29 entities Detail

Interaction partners 1. Hepatitis C Virus p7, : 8 interactors Detail

More details for 8 interactors identified by 5 citations

Experiments performed 4 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints, RDC restraints	combined_25181_2mts.nef
Input source #2: Coordindates	2mts.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---
ALENLVVLNAASVAGAHGILSFLVFFSAAWYIKGRLAPGAAYAFYGVWPLLLLLLALPPRAYA
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ALENLVVLNAASVAGAHGILSFLVFFSAAWYIKGRLAPGAAYAFYGVWPLLLLLLALPPRAYA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	63	0	0	100.0

Content subtype: combined_25181_2mts.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	177		96.8 (chain: A, length: 63)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	80 (80)	.	76.2 (chain: A, length: 63)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_2	OK	53 (53)	.	84.1 (chain: A, length: 63)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 96.8%
- Total number of assignments
  - ¹³C chemical shifts: 61
  - ¹H chemical shifts: 58
  - ¹⁵N chemical shifts: 58
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	303	61	20.1
¹H chemical shifts	367	58	15.8
¹⁵N chemical shifts	65	58	89.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	126	61	48.4
¹H chemical shifts	127	58	45.7
¹⁵N chemical shifts	59	58	98.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	177	0	0.0
¹H chemical shifts	240	0	0.0
¹⁵N chemical shifts	6	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	54	0	0.0
¹H chemical shifts	54	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	48	0	0.0
¹H chemical shifts	50	0	0.0
¹⁵N chemical shifts	2	0	0.0

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 76.2%
- Total number of restraints: 80
- Total number of restraints per polymer type: 80
- Weight of restraints: 1.0 (80)
- Potential type of restraints: square-well-parabolic (80)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 84.1%
- Total number of restraints: 53
- Potential type of restraints: undefined (53)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords membrane protein, viroporin, two transmembrane, ion channel

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Found 1 Document (0.606 seconds)

BMRB: 25181

Sample #1

Sample #2

Related entities 1. Hepatitis C Virus p7, : 1 : 4 : 29 entities Detail

Interaction partners 1. Hepatitis C Virus p7, : 8 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail