BMRB Entry 21097

Name: Structure of fungicidal Amphotericin B Sponge
Published: 2021-09-28

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR21097

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of fungicidal Amphotericin B Sponge

Deposition date:

2021-04-23

Original release date:

2021-09-28

Authors:

Lewandowska, Agnieszka; Soutar, Corinne; Greenwood, Alexander; Nimerovsky, Evgeny; De Lio, Ashley; Holler, Jordan; Hisao, Grant; Khandelwal, Anuj; Zhang, Jiabao; SantaMaria, Anna; Schwieters, Charles; Pogorelov, Taras; Burke, Martin; Rienstra, Chad

Citation:

Citation: Lewandowska, Agnieszka; Soutar, Corinne; Greenwood, Alexander; Nimerovsky, Evgeny; De Lio, Ashley; Holler, Jordan; Hisao, Grant; Khandelwal, Anuj; Zhang, Jiabao; SantaMaria, Anna; Schwieters, Charles; Pogorelov, Taras; Burke, Martin; Rienstra, Chad. "Fungicidal Amphotericin B Sponges are Assemblies of Staggered Asymmetric Head-to-Tail Homodimers Encasing Large Void Volumes" Nat. Struct. Mol. Biol. ., .-..

Assembly members:

Assembly members:
AmB, non-polymer, Formula weight is not available

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	66

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	AMFA	1
2	AMFB	1

Entities:

Entity 1, AMFA 1 residues - Formula weight is not available

1

UVR

Samples:

U13C_AmB: Amphotericin B, [U-13C], 100 ± 2 %

20_U13C_AmB: Amphotericin B U-13C, [U-13C], 20 ± 2 %; Amphotericin B NA 80 ± 2 %

skip13C_AmB: Amphotericin B, skip-13C, 100 ± 2 %

AmB_100_U-13C: pH: 7; temperature: 273.15 K

AmB_20_U-13C: pH: 7; temperature: 273.15 K

AmB_skip-13C: pH: 7; temperature: 273.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 13C-13C SPC q60	U13C_AmB	isotropic	AmB_100_U-13C
2D 13C-13C SPC DARR 50 ms	U13C_AmB	isotropic	AmB_100_U-13C
2D 13C-13C SPC DARR 100 ms	U13C_AmB	isotropic	AmB_100_U-13C
2D 13C-13C SPC DARR 200 ms	U13C_AmB	isotropic	AmB_100_U-13C
2D 13C-13C SPC DARR 500 ms	skip13C_AmB	isotropic	AmB_skip-13C
2D 13C-13C SPC DARR 900 ms	U13C_AmB	isotropic	AmB_100_U-13C
2D 13C-13C SPC DARR 1000 ms	skip13C_AmB	isotropic	AmB_skip-13C
2D 13C-13C SPC DARR 1500 ms	skip13C_AmB	isotropic	AmB_skip-13C
2D 13C-13C SPC PAR 5.5 ms	U13C_AmB	isotropic	AmB_100_U-13C
2D 13C-13C SPC PAR 11 ms	U13C_AmB	isotropic	AmB_100_U-13C
3D 13C-13C-13C SPC5 DARR 200 ms	U13C_AmB	isotropic	AmB_100_U-13C
3D 13C-13C-13C SPC5 PAR 11 ms	U13C_AmB	isotropic	AmB_100_U-13C
2D 14N-13C PM-RESPDOR	skip13C_AmB	isotropic	AmB_skip-13C
2D 13C-13C PAR DIL 11 ms	20_U13C_AmB	isotropic	AmB_20_U-13C

Software:

NMRPipe, Frank Delaglio, Stephan Grzesiek, Geerten. W. Vuister, Guang Zhu, John. Pfeifer, and Ad Bax, J. Biomol. NMR. 6, 277-293 (1995). - processing

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL. Bioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 - data analysis

VnmrJ, Agilent Technologies, Inc. 2014 - collection

SpinSight, Agilent Technologies, Inc. 2014 - collection

XPLOR-NIH v2.53, Schwieters, C. D., Kuszewski, J. J. & Marius Clore, G. Progress in Nuclear Magnetic Resonance Spectroscopy (2006) - structure calculations

Matlab, MATLAB R2015a. (2015). - geometry optimization

NMR spectrometers:

Varian VNMRS 750 MHz
Varian InfinityPlus 600 MHz
Varian InfinityPlus 600 MHz