BMRB Entry 19261

Name: HIV capsid dimer structure
Published: 2013-12-09

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PDB ID: 2m8l
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19261
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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:

HIV capsid dimer structure

Deposition date:

2013-05-23

Original release date:

2013-12-09

Authors:

Deshmukh, Lalit; Schwieters, Charles; Grishaev, Alexander; Clore, G. Marius; Ghirlando, Rodolfo

Citation:

Citation: Deshmukh, Lalit; Schwieters, Charles; Grishaev, Alexander; Ghirlando, Rodolfo; Baber, James; Clore, G. Marius. "Structure and Dynamics of Full-Length HIV-1 Capsid Protein in Solution." J. Am. Chem. Soc. 135, 16133-16147 (2013).
PubMed: 24066695

Assembly members:

Assembly members:
HIVcapsid, polymer, 231 residues, 24654.443 Da.

Natural source:

Natural source: Common Name: HIV Taxonomy ID: 12721 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus Human immunodeficiency virus

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HIVcapsid: PIVQNLQGQMVHQAISPRTL NAWVKVVEEKAFSPEVIPMF SALSEGATPQDLNTMLNTVG GHQAAMQMLKETINEEAAEW DRLHPVHAGPIAPGQMREPR GSDIAGTTSTLQEQIGWMTH NPPIPVGEIYKRWIILGLNK IVRMYSPTSILDIRQGPKEP FRDYVDRFYKTLRAEQASQE VKNWMTETLLVQNANPDCKT ILKALGPGATLEEMMTACQG VGGPGHKARVL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	563
15N chemical shifts	178
1H chemical shifts	178

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HIV capsid, 1	1
2	HIV capsid, 2	1

Entities:

Entity 1, HIV capsid, 1 231 residues - 24654.443 Da.

1

PRO

ILE

VAL

GLN

ASN

LEU

GLN

GLY

GLN

MET

2

VAL

HIS

GLN

ALA

ILE

SER

PRO

ARG

THR

LEU

3

ASN

ALA

TRP

VAL

LYS

VAL

GLU

LYS

4

ALA

PHE

SER

PRO

GLU

VAL

ILE

PRO

MET

PHE

5

SER

ALA

LEU

SER

GLU

GLY

ALA

THR

PRO

GLN

6

ASP

LEU

ASN

THR

MET

LEU

ASN

THR

VAL

GLY

7

GLY

HIS

GLN

ALA

MET

GLN

MET

LEU

LYS

8

GLU

THR

ILE

ASN

GLU

ALA

GLU

TRP

9

ASP

ARG

LEU

HIS

PRO

VAL

HIS

ALA

GLY

PRO

10

ILE

ALA

PRO

GLY

GLN

MET

ARG

GLU

PRO

ARG

11

GLY

SER

ASP

ILE

ALA

GLY

THR

SER

THR

12

LEU

GLN

GLU

GLN

ILE

GLY

TRP

MET

THR

HIS

13

ASN

PRO

ILE

PRO

VAL

GLY

GLU

ILE

TYR

14

LYS

ARG

TRP

ILE

LEU

GLY

LEU

ASN

LYS

15

ILE

VAL

ARG

MET

TYR

SER

PRO

THR

SER

ILE

16

LEU

ASP

ILE

ARG

GLN

GLY

PRO

LYS

GLU

PRO

17

PHE

ARG

ASP

TYR

VAL

ASP

ARG

PHE

TYR

LYS

18

THR

LEU

ARG

ALA

GLU

GLN

ALA

SER

GLN

GLU

19

VAL

LYS

ASN

TRP

MET

THR

GLU

THR

LEU

20

VAL

GLN

ASN

ALA

ASN

PRO

ASP

CYS

LYS

THR

21

ILE

LEU

LYS

ALA

LEU

GLY

PRO

GLY

ALA

THR

22

LEU

GLU

MET

THR

ALA

CYS

GLN

GLY

23

VAL

GLY

PRO

GLY

HIS

LYS

ALA

ARG

VAL

24

LEU

Samples:

sample_1: HIVcapsid, [U-13C; U-15N; U-2H], 0.5 mM; EDTA 1 mM; sodium chloride 50 mM; DTT 1 mM; sodium phosphate 20 mM; H2O 95%; D2O, [U-100% 2H], 5%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 308 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
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	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 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D TROSY-Artsy	sample_1	isotropic	sample_conditions_1
2D 1H-15N R1	sample_1	isotropic	sample_conditions_1
2D 1H-15N R1	sample_1	isotropic	sample_conditions_1
2D 1H-15N R1r	sample_1	isotropic	sample_conditions_1
2D 1H-15N R1r	sample_1	isotropic	sample_conditions_1
2D 1H-15N HetNOE	sample_1	isotropic	sample_conditions_1
2D 1H-15N HetNOE	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR NIH v2.32, Schwieters, Kuszewski, Tjandra and Clore - refinement

TOPSPIN v1.3, Bruker Biospin - collection

CCPN-Analysis v2.2.2, (CCPN-Analysis)-Vranken, Boucher, Stevens..Laue. - data analysis

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 500 MHz

BMRB	17738 19264 19575 25532
PDB	1AFV 1AK4 1E6J 1GWP 1L6N 1M9C 1M9E 1M9F 1M9X 1M9Y 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 2GOL 2JPR 2LF4 2M8L 2M8N 2M8P 2PWM 2PWO 2PXR 2X2D 2X83 3DIK 3GV2 3H47 3H4E 3J34 3J4F 3MGE 3NTE 3P05 3P0A 4ARG 4B4N 4D1K 4E91 4E92 4INB 4J93 4LQW 4NX4 4QNB 4U0A 4U0B 4U0C 4U0D 4U0E 4U0F 4USN 4WYM 4XFX 4XFY 4XFZ
DBJ	BAA00992 BAA12988 BAA12996 BAA93773 BAA93774
EMBL	CAA06946 CAA11884 CAA11886 CAA25902 CAA65355
GB	AAA44201 AAA44225 AAA44306 AAA44652 AAA44691
PIR	FOVWLV
PRF	1102247B 1103299C
REF	NP_057849 NP_057850 NP_579880
SP	P03347 P03348 P03349 P03366 P03367
AlphaFold	P03347 P03348 P03349 P03366 P03367