BMRB Entry 25255

Name: Denatured state of HIV-1 protease
Published: 2022-05-12

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25255

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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:

Denatured state of HIV-1 protease

Deposition date:

2014-09-30

Original release date:

2022-05-12

Authors:

Roesner, Heike; Caldarini, Martina; Vanoni, Maria; Aliverti, Alessandro; Broglia, Ricardo; Malmodin, Daniel; Kragelund, Birthe

Citation:

Citation: Rosner, Heike; Caldarini, Martina; Potel, Gregory; Malmodin, Daniel; Vanoni, Maria; Aliverti, Alessandro; Broglia, Ricardo; Kragelund, Birthe; Tiana, Guido. "The denatured state of HIV-1 protease under native conditions" Proteins 90, 96-109 (2022).
PubMed: 34312913

Assembly members:

Assembly members:
HIV-1_Protease, polymer, 95 residues, Formula weight is not available

Natural source:

Natural source: Common Name: HIV-1 Taxonomy ID: 11676 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus HIV-1

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET11a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HIV-1_Protease: PQITLWKRPLVTIRIGGQLK EALLNTGADDTVLEEMNLPG KWKPKMIGGIGGFIKVRQYD QIPVEIAGHKAIGTVLVGPT PVNIIGRNLLTQIGA

Data sets:

assigned_chemical_shifts
heteronucl_NOEs
heteronucl_T1_relaxation
heteronucl_T2_relaxation
theoretical_chem_shifts
- D0_theoretical_chem_shift_list_1

Data type	Count
13C chemical shifts	894
15N chemical shifts	439
1H chemical shifts	439
T1 relaxation values	424
T2 relaxation values	419
heteronuclear NOE values	425
theoretical chemical shifts	348

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HIV-1 Protease	1

Entities:

Entity 1, HIV-1 Protease 95 residues - Formula weight is not available

1

PRO

GLN

ILE

THR

LEU

TRP

LYS

ARG

PRO

LEU

2

VAL

THR

ILE

ARG

ILE

GLY

GLN

LEU

LYS

3

GLU

ALA

LEU

ASN

THR

GLY

ALA

ASP

4

THR

VAL

LEU

GLU

MET

ASN

LEU

PRO

GLY

5

LYS

TRP

LYS

PRO

LYS

MET

ILE

GLY

ILE

6

GLY

PHE

ILE

LYS

VAL

ARG

GLN

TYR

ASP

7

GLN

ILE

PRO

VAL

GLU

ILE

ALA

GLY

HIS

LYS

8

ALA

ILE

GLY

THR

VAL

LEU

VAL

GLY

PRO

THR

9

PRO

VAL

ASN

ILE

GLY

ARG

ASN

LEU

10

THR

GLN

ILE

GLY

ALA

Samples:

buffer: sodium phosphate 20 mM; HIV-1 Protease, [U-100% 13C; U-100% 15N], 200 uM; DSS 125 uM

Urea_8M: sodium phosphate 20 mM; HIV-1 Protease, [U-100% 13C; U-100% 15N], 200 uM; DSS 125 uM; urea 8 M

Urea_4M: sodium phosphate 20 mM; HIV-1 Protease, [U-100% 13C; U-100% 15N], 200 uM; DSS 125 uM; urea 4 M

GdHCl_1M: sodium phosphate 20 mM; HIV-1 Protease, [U-100% 13C; U-100% 15N], 200 uM; DSS 125 uM; Guanidine 1 M

aceticacid_25: sodium phosphate 20 mM; HIV-1 Protease, [U-100% 13C; U-100% 15N], 200 uM; DSS 125 uM; acetic acid 25%

25C_pH6_lowIS: ionic strength: 0.02 M; pH: 6.00; pressure: 1 atm; temperature: 298.15 K

25C_pH6_highIS: ionic strength: 1 M; pH: 6.00; pressure: 1 atm; temperature: 298.15 K

5C_pH6_lowIS: ionic strength: 0.02 M; pH: 6.00; pressure: 1 atm; temperature: 278.15 K

25C_pH2_lowIS: ionic strength: 0.02 M; pH: 2.00; pressure: 1 atm; temperature: 278.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	Urea_4M	isotropic	25C_pH6_lowIS
3D HNCA	Urea_4M	isotropic	25C_pH6_lowIS
3D HN(CO)CA	Urea_4M	isotropic	25C_pH6_lowIS
3D HNCO	Urea_4M	isotropic	25C_pH6_lowIS
3D CBCA(CO)NH	Urea_4M	isotropic	25C_pH6_lowIS
3D HNCACB	Urea_4M	isotropic	25C_pH6_lowIS
2D 1H-15N HSQC	Urea_8M	isotropic	25C_pH6_lowIS
3D HNCA	Urea_8M	isotropic	25C_pH6_lowIS
3D HN(CO)CA	Urea_8M	isotropic	25C_pH6_lowIS
3D HNCO	Urea_8M	isotropic	25C_pH6_lowIS
3D CBCA(CO)NH	Urea_8M	isotropic	25C_pH6_lowIS
3D HNCACB	Urea_8M	isotropic	25C_pH6_lowIS
2D 1H-15N HSQC	GdHCl_1M	isotropic	25C_pH6_highIS
3D HNCA	GdHCl_1M	isotropic	25C_pH6_highIS
3D HN(CO)CA	GdHCl_1M	isotropic	25C_pH6_highIS
3D HNCO	GdHCl_1M	isotropic	25C_pH6_highIS
3D CBCA(CO)NH	GdHCl_1M	isotropic	25C_pH6_highIS
3D HNCACB	GdHCl_1M	isotropic	25C_pH6_highIS
2D 1H-15N HSQC	aceticacid_25	isotropic	25C_pH2_lowIS
3D HNCA	aceticacid_25	isotropic	25C_pH2_lowIS
3D HN(CO)CA	aceticacid_25	isotropic	25C_pH2_lowIS
3D HNCO	aceticacid_25	isotropic	25C_pH2_lowIS
3D CBCA(CO)NH	aceticacid_25	isotropic	25C_pH2_lowIS
3D HNCACB	aceticacid_25	isotropic	25C_pH2_lowIS
2D 1H-15N HSQC	buffer	isotropic	5C_pH6_lowIS
3D HNCA	buffer	isotropic	5C_pH6_lowIS
3D HN(CO)CA	buffer	isotropic	5C_pH6_lowIS
3D HNCO	buffer	isotropic	5C_pH6_lowIS
3D CBCA(CO)NH	buffer	isotropic	5C_pH6_lowIS
3D HNCACB	buffer	isotropic	5C_pH6_lowIS
gNNOE (N15-NOE (TROSY))	Urea_4M	isotropic	25C_pH6_lowIS
gNNOE (N15-NOE (TROSY))	Urea_8M	isotropic	25C_pH6_lowIS
gNNOE (N15-NOE (TROSY))	GdHCl_1M	isotropic	25C_pH6_highIS
gNNOE (N15-NOE (TROSY))	aceticacid_25	isotropic	25C_pH2_lowIS
gNNOE (N15-NOE (TROSY))	buffer	isotropic	5C_pH6_lowIS
gNhsqc	Urea_4M	isotropic	25C_pH6_lowIS
gNhsqc	Urea_8M	isotropic	25C_pH6_lowIS
gNhsqc	GdHCl_1M	isotropic	25C_pH6_highIS
gNhsqc	aceticacid_25	isotropic	25C_pH2_lowIS
gNhsqc	buffer	isotropic	5C_pH6_lowIS

Software:

CCPN, CCPN - chemical shift assignment, peak picking

VNMRJ, Varian - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Agilent DD2 800 MHz
Varian INOVA 750 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks