BMRBj - BMREntryMaster

Found 1 Document (0.448 seconds)

BMRB: 19402

2MBJ

Structure of an antiparallel (2+2) G-quadruplex formed by human telomeric repeats in Na+ solution (with G22-to-BrG substitution)

Authors

Lim, K., Ng, V., Martin-Pintado, N., Heddi, B., Phan, A.

Assembly

antiparallel (2+2) G-quadruplex

Entity

1. antiparallel (2+2) G-quadruplex (polymer, Thiol state: not present), 27 monomers, 8655.341 Da Detail

TTAGGGTTAG GGTTAGGGTT AXGGTTA

Formula weight

8655.341 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.3 %, Completeness: 83.6 %, Completeness (bb): 83.5 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	83.6 % (204 of 244)	83.6 % (204 of 244)
Suger, PO4	83.5 % (152 of 182)	83.5 % (152 of 182)
Nucleobase	83.9 % (52 of 62)	83.9 % (52 of 62)
Aromatic	80.8 % (42 of 52)	80.8 % (42 of 52)
Methyl	100.0 % (10 of 10)	100.0 % (10 of 10)

1. DNA (27-MER)

TTAGGGTTAG GGTTAGGGTT AXGGTTA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	DNA (27-MER)	natural abundance	1.0 ~ 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 7.0

#	Name	Isotope labeling	Type	Concentration
4	DNA (27-MER)	natural abundance		1.0 ~ 2.0 mM
5	D2O	natural abundance		100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
6	DNA (27-MER)	[U-2% 15N]	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 7.0

#	Name	Isotope labeling	Concentration
9	DNA (27-MER)	[U-100% 2H]	0.2 ~ 1.0 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %

Release date

2013-09-15

Citation

Structure of the human telomere in Na+ solution: an antiparallel (2+2) G-quadruplex scaffold reveals additional diversity
Lim, K., Ng, V., Martin-Pintado, N., Heddi, B., Phan, A.
Nucleic Acids Res. (2013), 41, 10556-10562, PubMed 23999095 , DOI 10.1093/nar/gkt771 , Abstract

Related entities 1. antiparallel (2+2) G-quadruplex, : 2 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
4	DNA (27-MER)	natural abundance		1.0 ~ 2.0 mM
5	D2O	natural abundance		100 %

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 7.0

#	Name	Isotope labeling	Concentration
1	DNA (27-MER)	natural abundance	1.0 ~ 2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

3 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
4	DNA (27-MER)	natural abundance		1.0 ~ 2.0 mM
5	D2O	natural abundance		100 %

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
4	DNA (27-MER)	natural abundance		1.0 ~ 2.0 mM
5	D2O	natural abundance		100 %

5 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
4	DNA (27-MER)	natural abundance		1.0 ~ 2.0 mM
5	D2O	natural abundance		100 %

6 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 7.0

#	Name	Isotope labeling	Concentration
1	DNA (27-MER)	natural abundance	1.0 ~ 2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

7 H-D EXCHANGE

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	DNA (27-MER)	natural abundance	1.0 ~ 2.0 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

8 15N-FILTERED

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
6	DNA (27-MER)	[U-2% 15N]	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 7.0

#	Name	Isotope labeling	Concentration
9	DNA (27-MER)	[U-100% 2H]	0.2 ~ 1.0 mM
10	H2O	natural abundance	90 %
11	D2O	natural abundance	10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19402_2mbj.nef
Input source #2: Coordindates	2mbj.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:21:DA:O3'	1:22:BGM:P	unknown	unknown	n/a
1:22:BGM:O3'	1:23:DG:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	22	BGM	8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates

Sequence alignments

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

--------10--------20-------
TTAGGGTTAGGGTTAGGGTTAXGGTTA
|||||||||||||||||||||||||||
TTAGGGTTAGGGTTAGGGTTAXGGTTA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	27	0	0	100.0

Content subtype: combined_19402_2mbj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	229		100.0 (chain: A, length: 27)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	48 (1)	noe	44.4 (chain: A, length: 27)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	841 (1)	undefined	100.0 (chain: A, length: 27)
3	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	3 (1)	undefined	14.8 (chain: A, length: 27)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	12 (12)	.	44.4 (chain: A, length: 27)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 229
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
22	BGM

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	244	204	83.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	182	152	83.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	52	83.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	10	10	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	21	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 44.4%
- Total number of restraints: 48
- Weight of restraints: 1.0 (48)
- Potential type of restraints: square-well-parabolic (48)
- Range of distance target values: 2.0, 2.9 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
  - Total number of restraints: 835
  - Weight of restraints: 1.0 (835)
  - Potential type of restraints: square-well-parabolic (835)
  - Range of distance target values: 2.4, 6.25 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_6
    - Status: Warning
    - Experiment type: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 14.8%
    - Total number of restraints: 3
    - Weight of restraints: 1.0 (3)
    - Potential type of restraints: square-well-parabolic (3)
    - Range of distance target values: 42.1, 42.1 (Å)
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 44.4%
- Total number of restraints: 12
- Total number of restraints per polymer type: 12
- Weight of restraints: 1.0 (12)
- Potential type of restraints: square-well-parabolic (12)
- Dihedral angle restraints per residue

Keywords anticancer targets, G-quadruplex, human telomere

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Found 1 Document (0.448 seconds)

BMRB: 19402

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. antiparallel (2+2) G-quadruplex, : 2 entities Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 6 contents Detail