6X63

Atomic-Resolution Structure of HIV-1 Capsid Tubes by Magic Angle Spinning NMR

SOLID-STATE NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	Exp1_CORD50ms	100 % [U-13C; U-15N] HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
2	Exp2_CORD500ms	100 % [U-13C; U-15N] HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 600
3	Exp3_DARR50ms	100 % [U-13C; U-15N] HIV-1 capsid protein	solid	2.4 M	6	1 atm	277
4	Exp4_NCA	100 % [U-13C; U-15N] HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
5	Exp5_NCA	100 % [U-13C; U-15N] HIV-1 capsid protein	solid	2.4 M	6	1 atm	277
6	Exp6_NCACX	100 % [U-13C; U-15N] HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
7	Exp7_NCACX	100 % [U-13C; U-15N] HIV-1 capsid protein	solid	2.4 M	6	1 atm	277
8	Exp8_NCOCX	100 % [U-13C; U-15N] HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
9	Exp9_NCOCX3d	100 % [U-13C; U-15N] HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 600
10	Exp10_CONCA3d	100 % [U-13C; U-15N] HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 600
11	Exp11_NCACX3d	100 % [U-13C; U-15N] HIV-1 capsid protein	solid	2.4 M	6	1 atm	277
12	Exp12_NCOCX3d	100 % [U-13C; U-15N] HIV-1 capsid protein	solid	2.4 M	6	1 atm	277
13	Exp13_CORD10ms	100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
14	Exp14_CORD20ms	100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
15	Exp15_CORD50ms	100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
16	Exp16_CORD100ms	100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
17	Exp17_CORD200ms	100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
18	Exp18_CORD300ms	100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
19	Exp19_CORD400ms	100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
20	Exp20_CORD500ms	100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
21	Exp21_CORD500ms	100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 600
22	Exp22_NCACX	100 % [1,6-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
23	Exp23_CORD25ms	100 % [2-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 500
24	Exp24_CORD500ms	100 % [2-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 500
25	Exp25_CORD500ms	100 % [2-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
26	Exp26_PAINCP	100 % [2-13C]-Glucose,U-15N HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
27	Exp27_CORD25ms	100 % 13C,15N-His HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 600
28	Exp28_R211	100 % 13C,15N-Tyr HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 600
29	Exp29_REDOR1ms	100 % 13C,15N-Tyr HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 600
30	Exp30_REDOR1.6ms	100 % 13C,15N-Tyr HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 600
31	Exp31_REDOR2ms	100 % 13C,15N-Tyr HIV-1 capsid protein	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 600
32	Exp32_CORD50ms	50 % 13C,15N-Ala HIV-1 capsid protein, 50 % 13C,15N-Ile HIV-1 capsid	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
33	Exp33_PDSD1s	50 % 13C,15N-Ala HIV-1 capsid protein, 50 % 13C,15N-Ile HIV-1 capsid	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
34	Exp34_CORD50ms	50 % 13C,15N-Ala HIV-1 capsid protein, 50 % 13C,15N-Val HIV-1 capsid	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
35	Exp35_CORD500ms	86 % HIV-1 capsid protein, 14 % U-13C,15N-CA HIV-1 capsid	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 600
36	Exp36_NHHC3ms	50 % [U-13C] HIV-1 capsid protein, 50 % [U-15N] HIV-1 capsid	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850
37	Exp37_NHHC5ms	50 % [U-13C] HIV-1 capsid protein, 50 % [U-15N] HIV-1 capsid	solid	2.4 M	6	1 atm	277	Bruker AVANCE III 850

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	850
2	Bruker	AVANCE III	600
3	Bruker	AVANCE III	500

NMR Refinement
Method	Details	Software
data-guided molecular dynamics	Authors state that a single set of chemical shifts, distance restraints, and dihedral angle restraints was used for all chains in the CA tube structure refinement. Due to this, the completeness of resonance assignments is not calculated correctly by the PDB validation tool. For correct assignment metrics, please refer to PDB entry 6WAP.	X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	inner turns of helical assembly
Conformers Calculated Total Number	87
Conformers Submitted Total Number	1
Representative Model	1 (minimized average structure)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin		Bruker Biospin
2	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	chemical shift assignment	CcpNmr Analysis		CCPN
4	peak picking	CcpNmr Analysis		CCPN
5	data analysis	Sparky		Goddard
6	structure calculation	TALOS		Cornilescu, Delaglio and Bax
7	structure calculation	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
8	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
9	structure calculation	NAMD	2.13	James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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6X63

Atomic-Resolution Structure of HIV-1 Capsid Tubes by Magic Angle Spinning NMR