BMRB Entry 30929

Name: Immature HIV-1 CACTD-SP1 lattice with Bevirimat (BVM) and Inositol hexakisphosphate (IP6)
Published: 2023-01-20

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PDB ID: 7r7p
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30929
MolProbity Validation Chart

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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:

Immature HIV-1 CACTD-SP1 lattice with Bevirimat (BVM) and Inositol hexakisphosphate (IP6)

Deposition date:

2021-06-25

Original release date:

2023-01-20

Authors:

Sarkar, S.; Zadrozny, K.; Zadorozhnyi, R.; Russell, R.; Quinn, C.; Kleinpeter, A.; Ablan, S.; Xu, C.; Perilla, J.; Ganser-Pornillos, B.; Pornillos, O.; Freed, E.; Gronenborn, A.; Polenova, T.

Citation:

Citation: Sarkar, Sucharita; Zadrozny, Kaneil; Zadorozhnyi, Roman; Russell, Ryan; Quinn, Caitlin; Kleinpeter, Alex; Ablan, Sherimay; Meshkin, Hamed; Perilla, Juan; Freed, Eric; Ganser-Pornillos, Barbie; Pornillos, Owen; Gronenborn, Angela; Polenova, Tatyana. "Structural basis of HIV-1 maturation inhibitor binding and activity" Nat. Commun. 14, 1237-1237 (2023).
PubMed: 36871077

Assembly members:

Assembly members:
entity_1, polymer, 102 residues, 11094.672 Da.
entity_2, non-polymer, 584.826 Da.
entity_IHP, non-polymer, 660.035 Da.

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 BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGSPTSILDIRQGPKEPFRD YVDRFYKTLRAEQASQEVKN WMTETLLVQNANPDCKTILK ALGPGATLEEMMTACQGVGG PGHKARVLAEAMSQVTNTAT IM

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	417
15N chemical shifts	102
1H chemical shifts	251

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1
3	unit_3	1
4	unit_4	1
5	unit_5	1
6	unit_6	1
7	unit_7	2
8	unit_8	3

Entities:

Entity 1, unit_1 102 residues - 11094.672 Da.

1

GLY

SER

PRO

THR

SER

ILE

LEU

ASP

ILE

2

ARG

GLN

GLY

PRO

LYS

GLU

PRO

PHE

ARG

ASP

3

TYR

VAL

ASP

ARG

PHE

TYR

LYS

THR

LEU

ARG

4

ALA

GLU

GLN

ALA

SER

GLN

GLU

VAL

LYS

ASN

5

TRP

MET

THR

GLU

THR

LEU

VAL

GLN

ASN

6

ALA

ASN

PRO

ASP

CYS

LYS

THR

ILE

LEU

LYS

7

ALA

LEU

GLY

PRO

GLY

ALA

THR

LEU

GLU

8

MET

THR

ALA

CYS

GLN

GLY

VAL

GLY

9

PRO

GLY

HIS

LYS

ALA

ARG

VAL

LEU

ALA

GLU

10

ALA

MET

SER

GLN

VAL

THR

ASN

THR

ALA

THR

11

ILE

MET

Entity 2, unit_7 - 584.826 Da.

1

2I4

Entity 3, unit_8 - C6 H18 O24 P6 - 660.035 Da.

1

IHP

Samples:

sample_1: HIV-1 CACTD-SP1, [U-100% 13C; U-100% 15N], 400 uM; IP6 400 uM; BVM 360 uM; NaCl 250 mM

sample_2: HIV-1 CACTD-SP1, [U-100% 13C; U-100% 15N; 99.9%-2H], 400 uM; IP6 400 uM; Bevirimat 360 uM; NaCl 250 mM

sample_conditions_1: ionic strength: 250 mM; pH: 8; pressure: 1 atm; temperature: 277.15 K

sample_conditions_2: ionic strength: 250 mM; pH: 8; pressure: 1 atm; temperature: 263.15 K

sample_conditions_3: ionic strength: 250 mM; pH: 8; pressure: 1 atm; temperature: 277.15 K

sample_conditions_4: ionic strength: 250 mM; pH: 8; pressure: 1 atm; temperature: 268.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D CORD 10 ms	sample_1	isotropic	sample_conditions_1
2D CORD 25 ms	sample_1	isotropic	sample_conditions_1
2D CORD 50 ms	sample_1	isotropic	sample_conditions_1
2D CORD 100 ms	sample_1	isotropic	sample_conditions_1
2D CORD 200 ms	sample_1	isotropic	sample_conditions_1
2D CORD 10 ms	sample_1	isotropic	sample_conditions_2
2D CORD 25 ms	sample_1	isotropic	sample_conditions_2
2D CORD 100 ms	sample_1	isotropic	sample_conditions_2
2D CORD 200 ms	sample_1	isotropic	sample_conditions_2
2D NCACX 50 ms	sample_1	isotropic	sample_conditions_1
2D NCACX 50 ms	sample_1	isotropic	sample_conditions_2
2D CORD 25 ms	sample_1	isotropic	sample_conditions_1
2D CORD 100 ms	sample_1	isotropic	sample_conditions_1
2D CORD 250 ms	sample_1	isotropic	sample_conditions_1
2D CORD 500 ms	sample_1	isotropic	sample_conditions_1
2D direct INADEQUATE	sample_1	isotropic	sample_conditions_1
2D PAIN CP	sample_1	isotropic	sample_conditions_1
2D CORD 50 ms	sample_2	isotropic	sample_conditions_4
2D HC CP HETCOR	sample_2	isotropic	sample_conditions_3
2D doubleREDOR HETCOR	sample_2	isotropic	sample_conditions_3
2D hNH HETCOR	sample_2	isotropic	sample_conditions_3
2D hPH HETCOR	sample_2	isotropic	sample_conditions_3
1D 31P direct polarization	sample_2	isotropic	sample_conditions_3
1D 31P cross polarization	sample_2	isotropic	sample_conditions_3
1D doubleREDOR	sample_2	isotropic	sample_conditions_3

Software:

TopSpin, Bruker Biospin - collection

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

NMRFAM-SPARKY v3.115, Lee, Tonelli and Markley - chemical shift assignment, data analysis

CcpNmr Analysis v2.4, CCPN - chemical shift assignment

TALOS-N, Shen and Bax - structure calculation

X-PLOR NIH v2.53, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE III 850 MHz
Bruker AVANCE III 600 MHz

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