BMRBj - BMREntryMaster

Found 1 Document (0.638 seconds)

BMRB: 17928

2LJB

Structure of the influenza AM2-BM2 chimeric channel

Authors

Pielak, R.M., Oxenoid, K., Chou, J.J.

Assembly

AM2-BM2

Entity

1. AM2-BM2 (polymer, Thiol state: not present), 35 monomers, 3800.328 × 4 Da Detail

RSNDSSDPLV VAASIIGILH FIAWTIGHLN QIKRG

Total weight

15201.312 Da

Max. entity weight

3800.328 Da

Source organism

Alphainfluenzavirus

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 74.3 %, Completeness: 23.7 %, Completeness (bb): 41.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	23.7 % (95 of 401)	16.6 % (34 of 205)	22.2 % (35 of 158)	68.4 % (26 of 38)
Backbone	41.3 % (86 of 208)	38.9 % (28 of 72)	31.4 % (32 of 102)	76.5 % (26 of 34)
Sidechain	5.8 % (13 of 225)	4.5 % (6 of 133)	8.0 % (7 of 88)	0.0 % (0 of 4)
Aromatic	0.0 % (0 of 30)	0.0 % (0 of 15)	0.0 % (0 of 14)	0.0 % (0 of 1)
Methyl	11.5 % (6 of 52)	11.5 % (3 of 26)	11.5 % (3 of 26)

1. influenza AM2-BM2 chimeric channel

RSNDSSDPLV VAASIIGILH FIAWTIGHLN QIKRG

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details triple labeled for assignment

#	Name	Isotope labeling	Concentration
1	AM2-BM2	[U-100% 13C; U-100% 15N; U-80% 2H]	1.2 mM
2	DHPC	natural abundance	300 mM
3	sodium phosphate	natural abundance	40 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details double labeled for NOESY spectra

#	Name	Isotope labeling	Concentration
6	influenza AM2-BM2 chimeric channel	[U-100% 13C; U-100% 15N]	1.4 mM
7	DHPC	natural abundance	300 mM
8	sodium phosphate	natural abundance	40 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details isotopically mixed sample for inter-monomer NOEs

#	Name	Isotope labeling	Concentration
11	influenza AM2-BM2 chimeric channel	[U-100% 15N; U-99% 2H]	0.8 mM
12	influenza AM2-BM2 chimeric channel	[U-15% 13C]	0.8 mM
13	DHPC	natural abundance	300 mM
14	sodium phosphate	natural abundance	40 mM
15	H2O	natural abundance	95 %
16	D2O	natural abundance	5 %

Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details aligned sample for RDC measurement

#	Name	Isotope labeling	Concentration
17	influenza AM2-BM2 chimeric channel	[U-100% 13C; U-100% 15N; U-80% 2H]	0.5 mM
18	DHPC	natural abundance	300 mM
19	sodium phosphate	natural abundance	40 mM
20	DNA nanotube	natural abundance	5.4 mg
21	H2O	natural abundance	95 %
22	D2O	natural abundance	5 %

Sample #5

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 15% 13C labeled protein for stereospecific assignment of methyl groups

#	Name	Isotope labeling	Concentration
23	influenza AM2-BM2 chimeric channel	[U-15% 13C]	1.5 mM
24	DHPC	natural abundance	300 mM
25	sodium phosphate	natural abundance	40 mM
26	H2O	natural abundance	95 %
27	D2O	natural abundance	5 %

Protein Blocks Logo

Calculated from 15 models in PDB: 2LJB, Strand ID: A, B, C, D Detail

Release date

2011-12-04

Citation

Structural investigation of rimantadine inhibition of the AM2-BM2 chimera channel of influenza viruses
Pielak, R.M., Oxenoid, K., Chou, J.J.
Structure (2011), 19, 1655-1663, PubMed 22078564 , DOI 10.1016/j.str.2011.09.003 , Abstract

Related entities 1. AM2-BM2, : 1 : 1 : 97 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details triple labeled for assignment

#	Name	Isotope labeling	Concentration
1	AM2-BM2	[U-100% 13C; U-100% 15N; U-80% 2H]	1.2 mM
2	DHPC	natural abundance	300 mM
3	sodium phosphate	natural abundance	40 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details double labeled for NOESY spectra

#	Name	Isotope labeling	Concentration
6	influenza AM2-BM2 chimeric channel	[U-100% 13C; U-100% 15N]	1.4 mM
7	DHPC	natural abundance	300 mM
8	sodium phosphate	natural abundance	40 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

3 3D HNCA

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details triple labeled for assignment

#	Name	Isotope labeling	Concentration
1	AM2-BM2	[U-100% 13C; U-100% 15N; U-80% 2H]	1.2 mM
2	DHPC	natural abundance	300 mM
3	sodium phosphate	natural abundance	40 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

4 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details double labeled for NOESY spectra

#	Name	Isotope labeling	Concentration
6	influenza AM2-BM2 chimeric channel	[U-100% 13C; U-100% 15N]	1.4 mM
7	DHPC	natural abundance	300 mM
8	sodium phosphate	natural abundance	40 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

5 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details double labeled for NOESY spectra

#	Name	Isotope labeling	Concentration
6	influenza AM2-BM2 chimeric channel	[U-100% 13C; U-100% 15N]	1.4 mM
7	DHPC	natural abundance	300 mM
8	sodium phosphate	natural abundance	40 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

6 3D 1H-13C NOESY aromatic

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details double labeled for NOESY spectra

#	Name	Isotope labeling	Concentration
6	influenza AM2-BM2 chimeric channel	[U-100% 13C; U-100% 15N]	1.4 mM
7	DHPC	natural abundance	300 mM
8	sodium phosphate	natural abundance	40 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

7 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details isotopically mixed sample for inter-monomer NOEs

#	Name	Isotope labeling	Concentration
11	influenza AM2-BM2 chimeric channel	[U-100% 15N; U-99% 2H]	0.8 mM
12	influenza AM2-BM2 chimeric channel	[U-15% 13C]	0.8 mM
13	DHPC	natural abundance	300 mM
14	sodium phosphate	natural abundance	40 mM
15	H2O	natural abundance	95 %
16	D2O	natural abundance	5 %

8 2D 1H-13C HSQC (28m CT)

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 15% 13C labeled protein for stereospecific assignment of methyl groups

#	Name	Isotope labeling	Concentration
23	influenza AM2-BM2 chimeric channel	[U-15% 13C]	1.5 mM
24	DHPC	natural abundance	300 mM
25	sodium phosphate	natural abundance	40 mM
26	H2O	natural abundance	95 %
27	D2O	natural abundance	5 %

9 Interleaved HSQC-TROSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details triple labeled for assignment

#	Name	Isotope labeling	Concentration
1	AM2-BM2	[U-100% 13C; U-100% 15N; U-80% 2H]	1.2 mM
2	DHPC	natural abundance	300 mM
3	sodium phosphate	natural abundance	40 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

10 Interleaved HSQC-TROSY

Instrument

Bruker DMX - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details aligned sample for RDC measurement

#	Name	Isotope labeling	Concentration
17	influenza AM2-BM2 chimeric channel	[U-100% 13C; U-100% 15N; U-80% 2H]	0.5 mM
18	DHPC	natural abundance	300 mM
19	sodium phosphate	natural abundance	40 mM
20	DNA nanotube	natural abundance	5.4 mg
21	H2O	natural abundance	95 %
22	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, RDC restraints	combined_17928_2ljb.nef
Input source #2: Coordindates	2ljb.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

--20-------30--------40--------50--
RSNDSSDPLVVAASIIGILHFIAWTIGHLNQIKRG
|||||||||||||||||||||||||||||||||||
RSNDSSDPLVVAASIIGILHFIAWTIGHLNQIKRG
--------10--------20--------30-----

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--20-------30--------40--------50--
RSNDSSDPLVVAASIIGILHFIAWTIGHLNQIKRG
|||||||||||||||||||||||||||||||||||
RSNDSSDPLVVAASIIGILHFIAWTIGHLNQIKRG
--------10--------20--------30-----

Entity_assembly_ID (NMR): C vs Auth_asym_ID (model): C

--20-------30--------40--------50--
RSNDSSDPLVVAASIIGILHFIAWTIGHLNQIKRG
|||||||||||||||||||||||||||||||||||
RSNDSSDPLVVAASIIGILHFIAWTIGHLNQIKRG
--------10--------20--------30-----

Entity_assembly_ID (NMR): D vs Auth_asym_ID (model): D

--20-------30--------40--------50--
RSNDSSDPLVVAASIIGILHFIAWTIGHLNQIKRG
|||||||||||||||||||||||||||||||||||
RSNDSSDPLVVAASIIGILHFIAWTIGHLNQIKRG
--------10--------20--------30-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	35	100.0
B	B	35	100.0
C	C	35	100.0
D	D	35	100.0

Content subtype: combined_17928_2ljb.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	78		74.3 (chain: A, length: 35)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	115 (1)	noe	74.3 (chain: A, length: 35)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	64 (1)	noe	34.3 (chain: A, length: 35), 34.3 (chain: B, length: 35), 34.3 (chain: C, length: 35), 34.3 (chain: D, length: 35)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	44 (44)	.	68.6 (chain: A, length: 35)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	26 (26)	.	74.3 (chain: A, length: 35)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 74.3%
- Total number of assignments
  - ¹H chemical shifts: 26
  - ¹³C chemical shifts: 26
  - ¹⁵N chemical shifts: 26
- 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 (%)
¹H chemical shifts	205	26	12.7
¹³C chemical shifts	158	26	16.5
¹⁵N chemical shifts	40	26	65.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	26	36.1
¹³C chemical shifts	70	26	37.1
¹⁵N chemical shifts	34	26	76.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	133	0	0.0
¹³C chemical shifts	88	0	0.0
¹⁵N chemical shifts	6	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	0	0.0
¹³C chemical shifts	26	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	0	0.0
¹³C chemical shifts	14	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 74.3%
- Total number of restraints: 115
- Weight of restraints: 1.0 (115)
- Potential type of restraints: square-well-parabolic (115)
- Range of distance target values: 2.2, 4.4 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: C
    None
  - Chain_ID: D
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 34.3%
    - Entity_assembly_ID: B, Chain length: 35, Sequence coverage: 34.3%
    - Entity_assembly_ID: C, Chain length: 35, Sequence coverage: 34.3%
    - Entity_assembly_ID: D, Chain length: 35, Sequence coverage: 34.3%
  - Total number of restraints: 64
  - Weight of restraints: 1.0 (64)
  - Potential type of restraints: square-well-parabolic (64)
  - Range of distance target values: 3.0, 4.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
    - Chain_ID: D
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 68.6%
- Total number of restraints: 44
- Total number of restraints per polymer type: 44
- Weight of restraints: 1.0 (44)
- Potential type of restraints: square-well-parabolic (44)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 74.3%
- Total number of restraints: 26
- Potential type of restraints: square-well-parabolic (26)
- Range of observed RDC values: -17.29, 7.17 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords AM2-BM2 chimera, influenza, M2 channel

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Found 1 Document (0.638 seconds)

BMRB: 17928

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Related entities 1. AM2-BM2, : 1 : 1 : 97 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 6 contents Detail