BMRB Entry 34145

Name: G-quadruplex of Human papillomavirus type 52
Published: 2018-06-06

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PDB ID: 5o4d
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34145
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:

G-quadruplex of Human papillomavirus type 52

Deposition date:

2017-05-29

Original release date:

2018-06-06

Authors:

Marusic, M.; Plavec, J.

Citation:

Citation: Marusic, Maja; Plavec, Janez. "Towards Understanding of Polymorphism of the G-rich Region of Human Papillomavirus Type 52" Molecules 24, E1294-E1294 (2019).
PubMed: 30987050

Assembly members:

Assembly members:
entity_1, polymer, 23 residues, 7276.684 Da.

Natural source:

Natural source: Common Name: Human papillomavirus type 52 Taxonomy ID: 10618 Superkingdom: Viruses Kingdom: not available Genus/species: Alphapapillomavirus Alphapapillomavirus 9

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGGTAGGGCAGGGGACACAG GGT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	27
1H chemical shifts	221

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 23 residues - 7276.684 Da.

1

DG

DT

DA

DG

DC

DA

2

DG

DA

DC

DA

DC

DA

DG

3

DG

DT

Samples:

sample_1: entity_1 1.2 ± 0.1 mM; potassium phosphate 10 ± 0.5 mM; potassium chloride 40 ± 0.5 mM

sample_2: entity_1 1.2 ± 0.1 mM; potassium phosphate 10 ± 0.5 mM; potassium chloride 40 ± 0.5 mM

sample_3: entity_1, 15N site-specifically labelled at 5%, 0.9 ± 0.1 mM; potassium phosphate 10 ± 0.5 mM; potassium chloride 40 ± 0.5 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D HP COSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_3	isotropic	sample_conditions_1

Software:

vnmrj v3., Agilent - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.115, Goddard - chemical shift assignment, data analysis, peak picking

AMBER v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

NMR spectrometers:

Varian VNMRS 800 MHz
Varian DD2 600 MHz