BMRB Entry 34049

Name: Structure of a Spumaretrovirus Gag central domain reveals an ancient retroviral capsid
Published: 2019-03-21

Click here to enlarge.

PDB ID: 5m1g
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34049
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Structure of a Spumaretrovirus Gag central domain reveals an ancient retroviral capsid

Deposition date:

2016-10-07

Original release date:

2019-03-21

Authors:

Nicastro, G.; Ball, N.; Taylor, I.

Citation:

Citation: Goldstone, D.; Flower, T.; Ball, N.; Sanz-Ramos, M.; Yap, M.; Ogrodowicz, R.; Stanke, N.; Reh, J.; Lindemann, D.; Stoye, J.; Taylor, I.. "A unique spumavirus Gag N-terminal domain with functional properties of orthoretroviral matrix and capsid." PLoS Pathog. 9, e1003376-e1003376 (2013).
PubMed: 23675305

Assembly members:

Assembly members:
entity_1, polymer, 99 residues, 10949.391 Da.

Natural source:

Natural source: Common Name: SFVcpz(hu) Taxonomy ID: 11963 Superkingdom: Viruses Kingdom: not available Genus/species: Spumavirus spumaretrovirus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: PET47B

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: RTHGTFPMHQLGNVIKGIVD QEGVATAYTLGMMLSGQNYQ LVSGIIRGYLPGQAVVTALQ QRLDQEIDDQTRAETFIQHL NAVYEILGLNARGQSIRLE

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	568
15N chemical shifts	93
1H chemical shifts	1851

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, 1	1
2	entity_1, 2	1

Entities:

Entity 1, entity_1, 1 99 residues - 10949.391 Da.

1

ARG

THR

HIS

GLY

THR

PHE

PRO

MET

HIS

GLN

2

LEU

GLY

ASN

VAL

ILE

LYS

GLY

ILE

VAL

ASP

3

GLN

GLU

GLY

VAL

ALA

THR

ALA

TYR

THR

LEU

4

GLY

MET

LEU

SER

GLY

GLN

ASN

TYR

GLN

5

LEU

VAL

SER

GLY

ILE

ARG

GLY

TYR

LEU

6

PRO

GLY

GLN

ALA

VAL

THR

ALA

LEU

GLN

7

GLN

ARG

LEU

ASP

GLN

GLU

ILE

ASP

GLN

8

THR

ARG

ALA

GLU

THR

PHE

ILE

GLN

HIS

LEU

9

ASN

ALA

VAL

TYR

GLU

ILE

LEU

GLY

LEU

ASN

10

ALA

ARG

GLY

GLN

SER

ILE

ARG

LEU

GLU

Samples:

sample_1: GAG protein, [U-13C; U-15N; U-2H], 0.5 mM; NaCl 20 mM; Tris 20 mM

sample_conditions_1: ionic strength: 40 mM; pH: 7; pressure: 1 Pa; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

CARA, Keller and Wuthrich - chemical shift assignment

ARIA, Linge, O'Donoghue and Nilges - structure calculation

NMR spectrometers:

Bruker Avance 950 MHz
Bruker Avance 800 MHz
Bruker Avance 700 MHz
Bruker Avance 6 MHz