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BMRB: 18847

2M18

Structure of stacked G-quadruplex formed by human TERRA sequence in potassium solution

Authors

Martadinata, H., Phan, A.

Assembly

stacked G-quadruplex formed by human TERRA sequence

Entity

1. stacked G-quadruplex formed by human TERRA sequence (polymer, Thiol state: not present), 10 monomers, 3336.952 × 4 Da Detail

GGGUUAGGGU

Total weight

13347.808 Da

Max. entity weight

3336.952 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 69.9 %, Completeness (bb): 75.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	69.9 % (58 of 83)	69.9 % (58 of 83)
Suger, PO4	75.0 % (45 of 60)	75.0 % (45 of 60)
Nucleobase	56.5 % (13 of 23)	56.5 % (13 of 23)
Aromatic	56.5 % (13 of 23)	56.5 % (13 of 23)

1. RNA (5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')

GGGUUAGGGU

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPGPGPUPUPAPGPGPGPU)-3')	natural abundance		1.25 mM
2	K+ solution	natural abundance		90 mM

Release date

2013-02-28

Citation

Structure of human telomeric RNA (TERRA): stacking of two G-quadruplex blocks in K(+) solution
Martadinata, H., Phan, A.
Biochemistry (2013), 52, 2176-2183, PubMed 23445442 , DOI 10.1021/bi301606u , Abstract

Experiments performed 5 experiments Detail

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18847_2m18.nef
Input source #2: Coordindates	2m18.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
GGGUUAGGGU
||||||||||
GGGUUAGGGU

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

--------20
GGGUUAGGGU
||||||||||
GGGUUAGGGU
--------10

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

--------30
GGGUUAGGGU
||||||||||
GGGUUAGGGU
--------10

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

--------40
GGGUUAGGGU
||||||||||
GGGUUAGGGU
--------10

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	10	100.0
B	B	10	100.0
C	C	10	100.0
D	D	10	100.0

Content subtype: combined_18847_2m18.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	58		100.0 (chain: A, length: 10)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	740 (1)	noe	100.0 (chain: A, length: 10), 100.0 (chain: B, length: 10), 100.0 (chain: C, length: 10), 100.0 (chain: D, length: 10)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	34 (1)	noe	40.0 (chain: A, length: 10), 40.0 (chain: B, length: 10), 40.0 (chain: C, length: 10), 40.0 (chain: D, length: 10)
3	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	22 (1)	noe	20.0 (chain: A, length: 10), 20.0 (chain: B, length: 10), 20.0 (chain: C, length: 10), 20.0 (chain: D, length: 10)
4	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	100 (1)	noe	80.0 (chain: A, length: 10), 80.0 (chain: B, length: 10), 80.0 (chain: C, length: 10), 80.0 (chain: D, length: 10)
5	Distance restraints	CNS/XPLOR_distance_constraints_7	OK	96 (1)	hbond	60.0 (chain: A, length: 10), 60.0 (chain: B, length: 10), 60.0 (chain: C, length: 10), 60.0 (chain: D, length: 10)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	40 (40)	.	100.0 (chain: A, length: 10), 100.0 (chain: B, length: 10), 100.0 (chain: C, length: 10), 100.0 (chain: D, length: 10)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 58
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	58	69.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	45	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	13	56.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	8	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: D, Chain length: 10, Sequence coverage: 100.0%
- Total number of restraints: 740
- Weight of restraints: 1.0 (740)
- Potential type of restraints: square-well-parabolic (740)
- Range of distance target values: 1.77, 7.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 40.0%
    - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 40.0%
    - Entity_assembly_ID: C, Chain length: 10, Sequence coverage: 40.0%
    - Entity_assembly_ID: D, Chain length: 10, Sequence coverage: 40.0%
  - Total number of restraints: 34
  - Weight of restraints: 1.0 (34)
  - Potential type of restraints: square-well-parabolic (34)
  - Range of distance target values: 4.58, 7.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
    - Chain_ID: D
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_6
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 20.0%
      - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 20.0%
      - Entity_assembly_ID: C, Chain length: 10, Sequence coverage: 20.0%
      - Entity_assembly_ID: D, Chain length: 10, Sequence coverage: 20.0%
    - Total number of restraints: 22
    - Weight of restraints: 1.0 (22)
    - Potential type of restraints: square-well-parabolic (22)
    - Range of distance target values: 5.5, 7.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
      - Chain_ID: C
      - Chain_ID: D
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_5
      - Status: OK
      - Experiment type: noe
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 80.0%
        --------10 GGGUUAGGGU |||  ||||| GGG..AGGGU
        Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 80.0%
        --------20 GGGUUAGGGU |||  ||||| GGG..AGGGU
        Entity_assembly_ID: C, Chain length: 10, Sequence coverage: 80.0%
        --------30 GGGUUAGGGU |||  ||||| GGG..AGGGU
        Entity_assembly_ID: D, Chain length: 10, Sequence coverage: 80.0%
        --------40 GGGUUAGGGU |||  ||||| GGG..AGGGU
      - Total number of restraints: 100
        Intra-residue restraints, i = j : 8
        Sequential restraints, | i - j | = 1 : 24
        Backbone-side chain: 8
        Side chain-side chain: 16
        Long range restraints, | i - j | >= 5 : 36
        Inter-chain restraints: 28
        Symmetric restraints: 4
      - Weight of restraints: 1.0 (100)
        Intra-residue restraints, i = j : 1.0 (8)
        Sequential restraints, | i - j | = 1 : 1.0 (24)
        Backbone-side chain: 1.0 (8)
        Side chain-side chain: 1.0 (16)
        Long range restraints, | i - j | >= 5 : 1.0 (36)
        Inter-chain restraints: 1.0 (28)
        Symmetric restraints: 1.0 (4)
      - Potential type of restraints: square-well-parabolic (100)
        Intra-residue restraints, i = j : square-well-parabolic (8)
        Sequential restraints, | i - j | = 1 : square-well-parabolic (24)
        Backbone-side chain: square-well-parabolic (8)
        Side chain-side chain: square-well-parabolic (16)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (36)
        Inter-chain restraints: square-well-parabolic (28)
        Symmetric restraints: square-well-parabolic (4)
      - Range of distance target values: 5.5, 7.0 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        Chain_ID: C
        Chain_ID: D
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
        Chain_ID_1: B - Chain_ID_2: B
        Chain_ID_1: C - Chain_ID_2: C
        Chain_ID_1: D - Chain_ID_2: D
        Chain_ID_1: A - Chain_ID_2: B
        Chain_ID_1: A - Chain_ID_2: C
        None
        Chain_ID_1: A - Chain_ID_2: D
        Chain_ID_1: B - Chain_ID_2: C
        Chain_ID_1: B - Chain_ID_2: D
        None
        Chain_ID_1: C - Chain_ID_2: D
      - Saveframe: CNS/XPLOR_distance_constraints_7
        Status: OK
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 60.0%
        --------10 GGGUUAGGGU |||   ||| GGG...GGG ---------
        Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 60.0%
        --------20 GGGUUAGGGU |||   ||| GGG...GGG ---------
        Entity_assembly_ID: C, Chain length: 10, Sequence coverage: 60.0%
        --------30 GGGUUAGGGU |||   ||| GGG...GGG ---------
        Entity_assembly_ID: D, Chain length: 10, Sequence coverage: 60.0%
        --------40 GGGUUAGGGU |||   ||| GGG...GGG ---------
        Total number of restraints: 96
        Total hydrogen bond restraints: 96
        Weight of restraints: 1.0 (96)
        Total hydrogen bond restraints: 1.0 (96)
        Potential type of restraints: square-well-parabolic (96)
        Total hydrogen bond restraints: square-well-parabolic (96)
        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
        Chain_ID: C
        Chain_ID: D
        Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
        Chain_ID_1: B - Chain_ID_2: B
        Chain_ID_1: C - Chain_ID_2: C
        Chain_ID_1: D - Chain_ID_2: D
        Chain_ID_1: A - Chain_ID_2: B
        Chain_ID_1: A - Chain_ID_2: C
        None
        Chain_ID_1: A - Chain_ID_2: D
        None
        Chain_ID_1: B - Chain_ID_2: C
        None
        Chain_ID_1: B - Chain_ID_2: D
        None
        Chain_ID_1: C - Chain_ID_2: D

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 10, Sequence coverage: 100.0%
  - Entity_assembly_ID: D, Chain length: 10, Sequence coverage: 100.0%
- Total number of restraints: 40
- Total number of restraints per polymer type: 40
- Weight of restraints: 1.0 (40)
- Potential type of restraints: square-well-parabolic (40)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D

Keywords human telomeric RNA, RNA G-quadruplex, stacked G-quadruplex

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Found 1 Document (0.66 seconds)

BMRB: 18847

Sample

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 8 contents Detail