BMRBj - BMREntryMaster

Found 1 Document (0.754 seconds)

BMRB: 17929

2LJC

Structure of the influenza AM2-BM2 chimeric channel bound to rimantadine

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

2. RIM (non-polymer, Thiol state: not present), 179.302 Da

Total weight

15380.613 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: 71.4 %, Completeness: 19.2 %, Completeness (bb): 32.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	19.2 % (77 of 401)	16.1 % (33 of 205)	12.7 % (20 of 158)	63.2 % (24 of 38)
Backbone	32.2 % (67 of 208)	36.1 % (26 of 72)	16.7 % (17 of 102)	70.6 % (24 of 34)
Sidechain	5.3 % (12 of 225)	5.3 % (7 of 133)	5.7 % (5 of 88)	0.0 % (0 of 4)
Aromatic	30.0 % (9 of 30)	33.3 % (5 of 15)	28.6 % (4 of 14)	0.0 % (0 of 1)
Methyl	0.0 % (0 of 52)	0.0 % (0 of 26)	0.0 % (0 of 26)

1. AM2-BM2

RSNDSSDPLV VAASIIGILH FIAWTIGHLN QIKRG

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5, Details triple labeled protein 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	RIM	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5, Details double labeled protein for NOE experiments

#	Name	Isotope labeling	Concentration
7	AM2-BM2	[U-100% 13C; U-100% 15N]	1.5 mM
8	DHPC	[U-99% 2H]	300 mM
9	sodium phosphate	natural abundance	40 mM
10	RIM	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5, Details perdeuterated sample for protein-drug NOEs

#	Name	Isotope labeling	Concentration
13	AM2-BM2	[U-100% 15N; U-99% 2H]	1.5 mM
14	DHPC	[U-99% 2H]	300 mM
15	sodium phosphate	natural abundance	40 mM
16	RIM	natural abundance	50 mM
17	H2O	natural abundance	95 %
18	D2O	natural abundance	5 %

Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5, Details mixed sample for inter-monomer NOEs

#	Name	Isotope labeling	Concentration
19	AM2-BM2	[U-100% 15N; U-99% 2H]	0.9 mM
20	AM2-BM2	[U-10% 13C]	0.9 mM
21	DHPC	[U-99% 2H]	300 mM
22	sodium phosphate	natural abundance	40 mM
23	RIM	natural abundance	50 mM
24	H2O	natural abundance	95 %
25	D2O	natural abundance	5 %

Sample #5

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5, Details 15% 13C labeled sample for assigning stereospecific methyl groups

#	Name	Isotope labeling	Concentration
26	AM2-BM2	[U-15% 13C]	1.4 mM
27	DHPC	[U-99% 2H]	300 mM
28	sodium phosphate	natural abundance	40 mM
29	RIM	natural abundance	50 mM
30	H2O	natural abundance	95 %
31	D2O	natural abundance	5 %

Sample #6

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5, Details aligned sample for RDC measurement

#	Name	Isotope labeling	Concentration
32	AM2-BM2	[U-100% 13C; U-100% 15N; U-80% 2H]	0.5 mM
33	DHPC	natural abundance	300 mM
34	sodium phosphate	natural abundance	40 mM
35	RIM	natural abundance	50 mM
36	DNA nanotube	natural abundance	5.4 mg
37	H2O	natural abundance	95 %
38	D2O	natural abundance	5 %

Protein Blocks Logo

Calculated from 15 models in PDB: 2LJC, 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

Entries sharing articles BMRB: 1 entries Detail

BMRB: 17928 released on 2011-12-04
Title Structure of the influenza AM2-BM2 chimeric channel

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

Experiments performed 11 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 273 K, pH 7.5, Details triple labeled protein 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	RIM	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5, Details double labeled protein for NOE experiments

#	Name	Isotope labeling	Concentration
7	AM2-BM2	[U-100% 13C; U-100% 15N]	1.5 mM
8	DHPC	[U-99% 2H]	300 mM
9	sodium phosphate	natural abundance	40 mM
10	RIM	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	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 273 K, pH 7.5, Details triple labeled protein 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	RIM	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	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 273 K, pH 7.5, Details double labeled protein for NOE experiments

#	Name	Isotope labeling	Concentration
7	AM2-BM2	[U-100% 13C; U-100% 15N]	1.5 mM
8	DHPC	[U-99% 2H]	300 mM
9	sodium phosphate	natural abundance	40 mM
10	RIM	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	D2O	natural abundance	5 %

5 3D 1H-13C NOESY aliphatic

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5, Details double labeled protein for NOE experiments

#	Name	Isotope labeling	Concentration
7	AM2-BM2	[U-100% 13C; U-100% 15N]	1.5 mM
8	DHPC	[U-99% 2H]	300 mM
9	sodium phosphate	natural abundance	40 mM
10	RIM	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	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 273 K, pH 7.5, Details double labeled protein for NOE experiments

#	Name	Isotope labeling	Concentration
7	AM2-BM2	[U-100% 13C; U-100% 15N]	1.5 mM
8	DHPC	[U-99% 2H]	300 mM
9	sodium phosphate	natural abundance	40 mM
10	RIM	natural abundance	50 mM
11	H2O	natural abundance	95 %
12	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 273 K, pH 7.5, Details perdeuterated sample for protein-drug NOEs

#	Name	Isotope labeling	Concentration
13	AM2-BM2	[U-100% 15N; U-99% 2H]	1.5 mM
14	DHPC	[U-99% 2H]	300 mM
15	sodium phosphate	natural abundance	40 mM
16	RIM	natural abundance	50 mM
17	H2O	natural abundance	95 %
18	D2O	natural abundance	5 %

8 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5, Details mixed sample for inter-monomer NOEs

#	Name	Isotope labeling	Concentration
19	AM2-BM2	[U-100% 15N; U-99% 2H]	0.9 mM
20	AM2-BM2	[U-10% 13C]	0.9 mM
21	DHPC	[U-99% 2H]	300 mM
22	sodium phosphate	natural abundance	40 mM
23	RIM	natural abundance	50 mM
24	H2O	natural abundance	95 %
25	D2O	natural abundance	5 %

9 2D 1H-13C HSQC (28m CT)

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5, Details 15% 13C labeled sample for assigning stereospecific methyl groups

#	Name	Isotope labeling	Concentration
26	AM2-BM2	[U-15% 13C]	1.4 mM
27	DHPC	[U-99% 2H]	300 mM
28	sodium phosphate	natural abundance	40 mM
29	RIM	natural abundance	50 mM
30	H2O	natural abundance	95 %
31	D2O	natural abundance	5 %

10 Interleaved HSQC-TROSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5, Details triple labeled protein 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	RIM	natural abundance	50 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

11 Interleaved HSQC-TROSY

Instrument

Bruker DMX - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 7.5, Details aligned sample for RDC measurement

#	Name	Isotope labeling	Concentration
32	AM2-BM2	[U-100% 13C; U-100% 15N; U-80% 2H]	0.5 mM
33	DHPC	natural abundance	300 mM
34	sodium phosphate	natural abundance	40 mM
35	RIM	natural abundance	50 mM
36	DNA nanotube	natural abundance	5.4 mg
37	H2O	natural abundance	95 %
38	D2O	natural abundance	5 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17929_2ljc.nef
Input source #2: Coordindates	2ljc.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

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
E	1	RIM	RIMANTADINE	Distance restraints

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_17929_2ljc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	62		68.6 (chain: A, length: 35)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	80 (1)	noe	65.7 (chain: A, length: 35)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	76 (1)	noe	37.1 (chain: A, length: 35), 37.1 (chain: B, length: 35), 37.1 (chain: C, length: 35), 37.1 (chain: D, length: 35), 100.0 (chain: E, length: 1)
3	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	12 (1)	noe	100.0 (chain: E, length: 1)
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	21 (21)	.	60.0 (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: 68.6%
- Total number of assignments
  - ¹H chemical shifts: 24
  - ¹³C chemical shifts: 14
  - ¹⁵N chemical shifts: 24
- 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	24	11.7
¹³C chemical shifts	158	14	8.9
¹⁵N chemical shifts	40	24	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	24	33.3
¹³C chemical shifts	70	14	20.0
¹⁵N chemical shifts	34	24	70.6

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: 65.7%
- Total number of restraints: 80
- Weight of restraints: 1.0 (80)
- Potential type of restraints: square-well-parabolic (80)
- Range of distance target values: 2.2, 4.3 (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
  - Chain_ID: E
    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: 37.1%
    - Entity_assembly_ID: B, Chain length: 35, Sequence coverage: 37.1%
    - Entity_assembly_ID: C, Chain length: 35, Sequence coverage: 37.1%
    - Entity_assembly_ID: D, Chain length: 35, Sequence coverage: 37.1%
    - Entity_assembly_ID: E, Chain length: 1, Sequence coverage: 100.0%
  - Total number of restraints: 76
  - Weight of restraints: 1.0 (76)
  - Potential type of restraints: square-well-parabolic (76)
  - Range of distance target values: 2.0, 4.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
    - Chain_ID: D
    - Chain_ID: E
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_6
    - Status: OK
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: E, Chain length: 1, Sequence coverage: 100.0%
    - Total number of restraints: 12
    - Weight of restraints: 1.0 (12)
    - Potential type of restraints: square-well-parabolic (12)
    - Range of distance target values: 4.0, 4.0 (Å)
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
      - Chain_ID: C
      - Chain_ID: D
      - Chain_ID: E
    - 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: 60.0%
- Total number of restraints: 21
- Potential type of restraints: square-well-parabolic (21)
- Range of observed RDC values: -8.29, 4.18 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords AM2-BM2 chimera, drug complex, influenza, M2 channel, rimantadine binding

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.754 seconds)

BMRB: 17929

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Entries sharing articles BMRB: 1 entries Detail

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

Experiments performed 11 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail