BMRB Entry 16612

Name: Solid-state NMR structure of the M2 transmembrane peptide of the influenza A virus in DMPC lipid bilayers bound to deuterated amantadine
Published: 2010-02-08

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PDB ID: 2kqt
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16612
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solid-state NMR structure of the M2 transmembrane peptide of the influenza A virus in DMPC lipid bilayers bound to deuterated amantadine

Deposition date:

2009-11-18

Original release date:

2010-02-08

Authors:

Cady, Sarah; Schmidt-Rohr, Klaus; Wang, Jun; Soto, Cinque; DeGrado, William; Hong, Mei

Citation:

Citation: Cady, Sarah; Schmidt-Rohr, Klaus; Wang, Jun; Soto, Cinque; Degrado, William; Hong, Mei. "Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers." Nature 463, 689-692 (2010).
PubMed: 20130653

Assembly members:

Assembly members:
M2-TM, polymer, 25 residues, Formula weight is not available
308, non-polymer, 151.249 Da.

Natural source:

Natural source: Common Name: Influenzavirus A Taxonomy ID: 197911 Superkingdom: Virus Kingdom: not available Genus/species: Influenzavirus A not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
M2-TM: SSDPLVVAASIIGILHLILW ILDRL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	29
15N chemical shifts	7

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	M2-TM_tetramer_monomer1	1
2	M2-TM_tetramer_monomer2	1
3	M2-TM_tetramer_monomer3	1
4	M2-TM_tetramer_monomer4	1
5	Amantadine	2

Entities:

Entity 1, M2-TM_tetramer_monomer1 25 residues - Formula weight is not available

1

SER

ASP

PRO

LEU

VAL

ALA

SER

2

ILE

GLY

ILE

LEU

HIS

LEU

ILE

LEU

TRP

3

ILE

LEU

ASP

ARG

LEU

Entity 2, Amantadine - C10 H17 N - 151.249 Da.

1

308

Samples:

SID-M2-TM_4x: M2-TM, [U-99% 13C; U-99% 15N] at S31, I32 and D44, 5.8 ± .1 mg; DMPC 21.6 ± .1 mg; NaH2PO4 10 mM; Na2HPO4 10 mM; EDTA 1 mM; NaN3 .1 mM; d15-1-aminoadamantane*HCl, [U-2H], .42 ± .05 mg

SID-M2-TM_1x: M2-TM, [U-99% 13C; U-99% 15N] at S31, I32 and D44, 5.0 ± .1 mg; DMPC 10.4 ± .1 mg; NaH2PO4 10 mM; Na2HPO4 10 mM; EDTA 1 mM; NaN3 0.1 mM; d15-1-aminoadamantane*HCl, [U-2H], 0.09 ± .05 mg

LVAG-M2-TM_4x: M2-TM, [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34, 5.2 ± .1 mg; DMPC 19.9 ± .1 mg; NaH2PO4 10 mM; Na2HPO4 10 mM; EDTA 1 mM; NaN3 .1 mM; d15-1-aminoadamantane*HCl, [U-2H], 0.38 ± .05 mg

Unlabeled-M2-TM_4x: M2-TM, [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34, 7 ± .1 mg; DMPC 27 ± .1 mg; NaH2PO4 10 mM; Na2HPO4 10 mM; EDTA 1 mM; NaN3 .1 mM; d15-1-aminoadamantane*HCl, [U-2H], 2.0 ± .05 mg

Unlabeled-M2-TM_1x: M2-TM, [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34, 7 ± .1 mg; DMPC 27 ± .1 mg; NaH2PO4 10 mM; Na2HPO4 10 mM; EDTA 1 mM; NaN3 .1 mM; d15-1-aminoadamantane*HCl, [U-2H], 0.5 ± .05 mg

sample_conditions_1: pH: 7.5; pressure: 1 atm; temperature: 243 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 13C-13C Spin Diffusion	SID-M2-TM_4x	solid	sample_conditions_1
2D 13C-13C Spin Diffusion	SID-M2-TM_1x	solid	sample_conditions_1
2D 13C-13C Spin Diffusion	LVAG-M2-TM_4x	solid	sample_conditions_1
2D 13C-15N HETCOR	SID-M2-TM_4x	solid	sample_conditions_1
2D 13C-15N HETCOR	SID-M2-TM_1x	solid	sample_conditions_1
2D 13C-15N HETCOR	LVAG-M2-TM_4x	solid	sample_conditions_1
1D 2H-13C REDOR, single 13C pulse	SID-M2-TM_4x	solid	sample_conditions_1
1D 2H-13C REDOR, single 13C pulse	SID-M2-TM_1x	solid	sample_conditions_1
1D 2H-13C REDOR, single 13C pulse	LVAG-M2-TM_4x	solid	sample_conditions_1
1D 2H-13C REDOR, single 13C pulse	SID-M2-TM_4x	solid	sample_conditions_1
1D 2H-13C REDOR, single 2H pulse	SID-M2-TM_4x	solid	sample_conditions_1
1D 2H-13C REDOR, single 2H pulse	SID-M2-TM_1x	solid	sample_conditions_1
1D 2H-13C REDOR, single 2H pulse	LVAG-M2-TM_4x	solid	sample_conditions_1
2H Static Quadrupolar Echo	Unlabeled-M2-TM_4x	solid	sample_conditions_1
2H Static Quadrupolar Echo	Unlabeled-M2-TM_1x	solid	sample_conditions_1
2H Static Quadrupolar Echo	LVAG-M2-TM_4x	solid	sample_conditions_1

Software:

TOPSPIN v1.3, Bruker Biospin - chemical shift assignment, collection, data analysis, peak picking, processing

MATLAB, The MathWorks - REDOR simulation

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

xwinnmr, Bruker Biospin - chemical shift assignment, collection

NMR spectrometers:

Bruker Avance 400 MHz
Bruker Avance 600 MHz

BMRB	25234
PDB	1MP6 1NYJ 2H95 2KQT 2L0J 2RLF 4QK7 4QKC 4QKL 4QKM
DBJ	BAB39517 BAB39519 BAD02354 BAD02364 BAD89308
EMBL	CAA30887 CAA30889 CAA30891 CAA30893 CAA41929
GB	AAA19192 AAA19194 AAA19196 AAA43091 AAA43276
PIR	JN0393 MMIV2 S04057 S04061 S14617
REF	NP_859035 YP_308670 YP_308840
SP	A4GBX8 A4GCH6 A4GCJ8 A4GCK9 A4U7A7
AlphaFold	A4GBX8 A4GCH6 A4GCJ8 A4GCK9 A4U7A7