BMRB Entry 34055

Name: C-terminal domain structure of VSG M1.1
Published: 2017-09-14

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PDB ID: 5m4t
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34055
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: C-terminal domain structure of VSG M1.1 PubMed: 28894098

Deposition date: 2016-10-19 Original release date: 2017-09-14

Authors: Jones, N.; Mott, H.; Carrington, M.

Citation: Bartossek, Thomas; Jones, Nicola; Schafer, Christin; Cvitkovic, Mislav; Glogger, Marius; Mott, Helen; Kuper, Jochen; Brennich, Martha; Carrington, Mark; Smith, Ana-Suncana; Fenz, Susanne; Kisker, Caroline; Engstler, Markus. "Structural basis for the shielding function of the dynamic trypanosome variant surface glycoprotein coat" Nat. Microbiol. 2, 1523-1532 (2017).

Assembly members:
Variant surface glycoprotein MITAT 1.1, polymer, 73 residues, 8156.062 Da.

Natural source: Common Name: kinetoplastids Taxonomy ID: 5702 Superkingdom: Eukaryota Kingdom: not available Genus/species: Trypanosoma brucei

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

Entity Sequences (FASTA):
Variant surface glycoprotein MITAT 1.1: GSKKQQTESAENKEKICNAA KDNQKACENLKEKGCVFNTE SNKCELKKDVKEKLEKESKE TEGKDEKANTTGS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
15N chemical shifts	81
1H chemical shifts	490

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 73 residues - 8156.062 Da.

1

GLY

SER

LYS

GLN

THR

GLU

SER

ALA

2

GLU

ASN

LYS

GLU

LYS

ILE

CYS

ASN

ALA

3

LYS

ASP

ASN

GLN

LYS

ALA

CYS

GLU

ASN

LEU

4

LYS

GLU

LYS

GLY

CYS

VAL

PHE

ASN

THR

GLU

5

SER

ASN

LYS

CYS

GLU

LEU

LYS

ASP

VAL

6

LYS

GLU

LYS

LEU

GLU

LYS

GLU

SER

LYS

GLU

7

THR

GLU

GLY

LYS

ASP

GLU

LYS

ALA

ASN

THR

8

THR

GLY

SER

Samples:

sample_1: Variant surface glycoprotein MITat1.1, [U-15N], 0.5 mM; sodium chloride 150 mM; sodium phosphate 50 mM; H2O 90%; D2O 10%

sample_2: Variant surface glycoprotein MITat1.1 0.5 mM; sodium chloride 150 mM; sodium phosphate 50 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 200 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNHA	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1

Software:

ANSIG, Kraulis - chemical shift assignment

AZARA, Boucher - processing

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

NMR spectrometers:

Bruker DRX 500 MHz
Bruker DRX 600 MHz
Bruker DRX 800 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts