BMRBj - BMREntryMaster

Found 1 Document (0.447 seconds)

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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.447 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