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BMRB: 17697

2LE6

Structure of a dimeric all-parallel-stranded G-quadruplex stacked via the 5'-to-5' interface

Authors

Do, N., Lim, K., Teo, M., Heddi, B., Phan, A.

Assembly

G-quadruplex

Entity

1. G-quadruplex (polymer, Thiol state: not present), 16 monomers, 5170.241 × 2 Da Detail

GXGTGGGTGG GTGGGT

Total weight

10340.482 Da

Max. entity weight

5170.241 Da

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.8 %, Completeness: 79.9 %, Completeness (bb): 77.1 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	79.9 % (111 of 139)	79.9 % (111 of 139)
Suger, PO4	77.1 % (81 of 105)	77.1 % (81 of 105)
Nucleobase	88.2 % (30 of 34)	88.2 % (30 of 34)
Aromatic	86.7 % (26 of 30)	86.7 % (26 of 30)
Methyl	100.0 % (4 of 4)	100.0 % (4 of 4)

1. DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')

GXGTGGGTGG GTGGGT

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	G-quadruplex	natural abundance		0.5 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	G-quadruplex	natural abundance		0.5 ~ 2.0 mM
5	D2O	natural abundance		100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
6	G-quadruplex	[U-2% 15N; U-2% 13C]		0.5 ~ 2.0 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
9	G-quadruplex	[U-100% 2H]		0.5 ~ 2.0 mM
10	H2O	natural abundance		90 %
11	D2O	natural abundance		10 %

Release date

2011-08-18

Citation

Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity
Do, N., Lim, K., Teo, M., Heddi, B., Phan, A.
Nucleic Acids Res. (2011), 39, 9448-9457, PubMed 21840903 , DOI 10.1093/nar/gkr539 , Abstract

Experiments performed 9 experiments Detail

1 2D 1H-13C JR HMBC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	G-quadruplex	natural abundance		0.5 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 2D 1H-1H JR NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	G-quadruplex	natural abundance		0.5 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	G-quadruplex	natural abundance		0.5 ~ 2.0 mM
5	D2O	natural abundance		100 %

4 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	G-quadruplex	natural abundance		0.5 ~ 2.0 mM
5	D2O	natural abundance		100 %

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	G-quadruplex	natural abundance		0.5 ~ 2.0 mM
5	D2O	natural abundance		100 %

6 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	G-quadruplex	natural abundance		0.5 ~ 2.0 mM
5	D2O	natural abundance		100 %

7 H-D exchange

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	G-quadruplex	natural abundance		0.5 ~ 2.0 mM
5	D2O	natural abundance		100 %

8 15N-filtered

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
6	G-quadruplex	[U-2% 15N; U-2% 13C]		0.5 ~ 2.0 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

9 D-labeled

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
9	G-quadruplex	[U-100% 2H]		0.5 ~ 2.0 mM
10	H2O	natural abundance		90 %
11	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17697_2le6.nef
Input source #2: Coordindates	2le6.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10------
GIGTGGGTGGGTGGGT
||||||||||||||||
GIGTGGGTGGGTGGGT

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10------
GIGTGGGTGGGTGGGT
||||||||||||||||
GIGTGGGTGGGTGGGT

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	16	0	0	100.0
B	B	16	0	0	100.0

Content subtype: combined_17697_2le6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	119		100.0 (chain: B, length: 16)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1066 (1)	noe	100.0 (chain: A, length: 16), 100.0 (chain: B, length: 16)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	92 (1)	hbond	75.0 (chain: A, length: 16), 75.0 (chain: B, length: 16)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	64 (64)	.	75.0 (chain: A, length: 16), 75.0 (chain: B, length: 16)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 119
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 100.0%
- Total number of restraints: 1066
- Weight of restraints: 1.0 (1066)
- Potential type of restraints: square-well-parabolic (1066)
- Range of distance target values: 2.7, 6.25 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 75.0%
    - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 75.0%
  - Total number of restraints: 92
  - Weight of restraints: 1.0 (92)
  - Potential type of restraints: square-well-parabolic (92)
  - Range of distance target values: 1.95, 2.95 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 16, Sequence coverage: 75.0%
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 75.0%
- Total number of restraints: 64
- Total number of restraints per polymer type: 64
- Weight of restraints: 1.0 (64)
- Potential type of restraints: square-well-parabolic (64)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords anticancer, G-quadruplex, HIV-1 integrase inhibition, stacking