BMRB Entry 17307

Name: NMR Structure of the monomeric mutant C-terminal domain of HIV-1 Capsid in complex with stapled peptide Inhibitor
Published: 2010-12-16

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PDB ID: 2l6e
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR17307
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR Structure of the monomeric mutant C-terminal domain of HIV-1 Capsid in complex with stapled peptide Inhibitor

Deposition date:

2010-11-18

Original release date:

2010-12-16

Authors:

Bhattacharya, Shibani; Zhang, Hongtao; Debnath, Asim; Cowburn, David

Citation:

Citation: Bhattacharya, Shibani; Zhang, Hongtao; Debnath, Asim; Cowburn, David. "Solution structure of a hydrocarbon stapled peptide inhibitor in complex with monomeric C-terminal domain of HIV-1 capsid." J. Biol. Chem. 283, 16247-16278 (2008).
PubMed: 18417468

Assembly members:

Assembly members:
Capsid_protein_p24, polymer, 105 residues, Formula weight is not available
NYAD-13_Peptide_Inhibitor, polymer, 14 residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET14b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Capsid_protein_p24: MGSSHHHHHHSSGLVPRGSH MTSILDIRQGPKEPFRDYVD RFYKTLRAEQASQEVKNAAT ETLLVQNANPDCKTILKALG PAATLEEMMTACQGVGGPGH KARVL
NYAD-13_Peptide_Inhibitor: ITFXDLLXYYGKKK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	377
15N chemical shifts	94
1H chemical shifts	713

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Capsid_protein_p24	1
2	NYAD-13_Peptide_Inhibitor	2

Entities:

Entity 1, Capsid_protein_p24 105 residues - Formula weight is not available

1

MET

GLY

SER

HIS

2

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

3

MET

THR

SER

ILE

LEU

ASP

ILE

ARG

GLN

GLY

4

PRO

LYS

GLU

PRO

PHE

ARG

ASP

TYR

VAL

ASP

5

ARG

PHE

TYR

LYS

THR

LEU

ARG

ALA

GLU

GLN

6

ALA

SER

GLN

GLU

VAL

LYS

ASN

ALA

THR

7

GLU

THR

LEU

VAL

GLN

ASN

ALA

ASN

PRO

8

ASP

CYS

LYS

THR

ILE

LEU

LYS

ALA

LEU

GLY

9

PRO

ALA

THR

LEU

GLU

MET

THR

10

ALA

CYS

GLN

GLY

VAL

GLY

PRO

GLY

HIS

11

LYS

ALA

ARG

VAL

LEU

Entity 2, NYAD-13_Peptide_Inhibitor 14 residues - Formula weight is not available

X=MK8 cis double bond between CE atoms of residue 4 and 8.

1

ILE

THR

PHE

MK8

ASP

LEU

MK8

TYR

2

GLY

LYS

Samples:

sample_1: Capsid protein p24, [U-100% 13C; U-100% 15N], 600 uM; NYAD-13 Peptide Inhibitor 900 uM; DTT 2 mM; ammonium acetate 100 mM; H2O 90%; D2O 10%

sample_2: Capsid protein p24, [U-100% 13C; U-100% 15N], 600 uM; NYAD-13 Peptide Inhibitor 900 uM; DTT 2 mM; ammonium acetate 100 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
2D f1,f2 filtered 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D f2 filtered 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

ARIA v2.2, Linge, O'Donoghue and Nilges - refinement

CARA v1.5, Keller, Wuthrich - chemical shift assignment, peak picking

TOPSPIN v1.3, Bruker Biospin - processing

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 900 MHz

BMRB	15137 16555 17738 19264 25532
PDB	1E6J 1VU4 1VU5 1VU6 1VU7 1VU8 1VU9 1VUA 1VUC 1VUD 1VUE 1VUF 1VUG 1VUH 1VUI 1VUJ 1VUK 1VUL 1VUM 1VUN 1VUO 1VUP 1VUQ 1VUR 1VUS 1VUT 1VUU 1VUV 1VUW 1VUX 1VUY 1VUZ 1VV0 1VV1 1VV2 1VV3 1VV4 1VV5 1VV6 1VV7 1VV8 1VV9 1VVA 1VVB 1VVF 1VVG 1VVH 1VVI 2JO0 2JYG 2JYL 2KOD 2L6E 2LF4 2M8P 3GV2 3H47 3H4E 3J34 3J4F 3MGE 3NTE 3P05 3P0A 4ARG 4QNB 4U0A 4U0B 4U0C 4U0D 4U0E 4U0F 4WYM
DBJ	BAA00992 BAA12988 BAA12996 BAA93785 BAA93786
EMBL	CAA82791 CAA82793 CAB85858 CAB85866 CAB87157
GB	AAA44201 AAA44306 AAA44652 AAA76686 AAB04036
PIR	FOVWLV
PRF	1102247B 1103299C
REF	NP_057849 NP_057850 NP_579880
SP	P03347 P03348 P03366 P03367 P04585
AlphaFold	P03347 P03348 P03366 P03367 P04585