BMRB Entry 4781

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PDB ID: 1f6u
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR4781
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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:

NMR Structure of Stem-loop SL2 of the HIV-1 Psi RNA Packaging Signal Reveals a Novel A-U-A Base-triple Platform

Deposition date:

2000-07-10

Original release date:

2002-04-04

Authors:

Amarasinghe, Gaya; De Guzman, Roberto; Turner, Ryan; Summers, Michael

Citation:

Citation: Amarasinghe, Gaya; De Guzman, Roberto; Turner, Ryan; Summers, Michael. "NMR Structure of Stem-loop SL2 of the HIV-1 Psi RNA Packaging Signal Reveals a Novel A-U-A Base-triple Platform" J. Mol. Biol. 299, 145-156 (2000).
PubMed: 10860728

Assembly members:

Assembly members:
HIV-1 SL2 stem loop, polymer, 19 residues, 6371 Da.
NCp7 protein, polymer, 55 residues, 6372 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HIV-1 SL2 stem loop: GGCGACUGGUGAGUACGCC
NCp7 protein: MQKGNFRNQRKTVKCFNCGK EGHIAKNCRAPRKKGCWKCG KEGHQMKDCTERQAN

Data sets:

assigned_chemical_shifts
- ncp7
- NCSL2_RNA

Data type	Count
13C chemical shifts	272
15N chemical shifts	58
1H chemical shifts	456

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SL2 RNA	1
2	NCp7	2

Entities:

Entity 1, SL2 RNA 19 residues - 6371 Da.

1

G

C

G

A

C

U

G

U

2

G

A

G

U

A

C

G

C

Entity 2, NCp7 55 residues - 6372 Da.

1

MET

GLN

LYS

GLY

ASN

PHE

ARG

ASN

GLN

ARG

2

LYS

THR

VAL

LYS

CYS

PHE

ASN

CYS

GLY

LYS

3

GLU

GLY

HIS

ILE

ALA

LYS

ASN

CYS

ARG

ALA

4

PRO

ARG

LYS

GLY

CYS

TRP

LYS

CYS

GLY

5

LYS

GLU

GLY

HIS

GLN

MET

LYS

ASP

CYS

THR

6

GLU

ARG

GLN

ALA

ASN

Samples:

sample_1: HIV-1 SL2 stem loop0.6 – 1.2 mM; NCp7 protein0.6 – 1.2 mM

sample_2: HIV-1 SL2 stem loop, [U-13C], 0.8 mM; NCp7 protein, [U-13C; U-15N], 0.8 mM

sample_3: HIV-1 SL2 stem loop0.8 – 1.2 mM; NCp7 protein, [U-15N], 0.8 – 1.2 mM

Ex-cond-1: pH*: 6.5; temperature: 298 K

Ex-cond-2: pH*: 6.5; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	not available	not available	not available
2D TOCSY	not available	not available	not available
2D DQF COSY	not available	not available	not available
1H-13C HMQC	not available	not available	not available
1H,1H,13C HMQC-NOESY	not available	not available	not available
1H,1H,13C HCCH-COSY	not available	not available	not available
1H,1H,13C HCCH-TOCSY	not available	not available	not available
1H,1H,15N HSQC-NOESY	not available	not available	not available

Software:

XWINNMR v2.6 - Data aquisition on from the NMR

NMRPipe v1.0 - Data processing

NMRView v3.0 - Data analysis

DYANA v1.5 - Structure calculation

CNS v1.0 - Structure refinement and energy minimization

NMR spectrometers:

Bruker Avance DMX 600 MHz
Bruker Avance DRX 800 MHz

DBJ	BAC02557 BAC77486 BAC77487 BAC77511 BAC77512
EMBL	CAD26937 CAD26939 CAD26945 CAD26946 CAD26947
GenBank	AAA44987 AAA81036 AAB60571 AAC28445 AAD03199
SWISS-PROT	P12493 P12497 P35962 P35963 Q73367