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Found 1 Document (0.448 seconds)

BMRB: 30258

5UZZ

Structure of wild type pre-miR21 apical loop

Authors

Shortridge, M.D., Varani, G.

Assembly

14-mer Peptide/RNA Complex

Entity

1. 14-mer Peptide/RNA Complex, entity 1 (polymer, Thiol state: not present), 31 monomers, 9975.865 Da Detail

GGUGUUGACU GUUGAAUCUC AUGGCAACAC C

2. 14-mer Peptide/RNA Complex, entity 2 (polymer, Thiol state: not present), 14 monomers, 1804.161 Da Detail

RVRTRGKRRI RRXP

Total weight

11780.026 Da

Max. entity weight

9975.865 Da

Source organism

Homo sapiens , synthetic construct

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 68.9 %, Completeness: 39.6 %, Completeness (bb): 45.5 % Detail

Polymer type: polyribonucleotide polypeptide(L)

	Total	¹H	¹⁵N
All	39.6 % (158 of 399)	42.7 % (158 of 370)	0.0 % (0 of 29)
Backbone	45.5 % (102 of 224)	48.1 % (102 of 212)	0.0 % (0 of 12)
Sidechain	32.0 % (56 of 175)	35.4 % (56 of 158)	0.0 % (0 of 17)
Aromatic	63.6 % (56 of 88)	78.9 % (56 of 71)	0.0 % (0 of 17)
Methyl	0.0 % (0 of 5)	0.0 % (0 of 5)

1. entity 1

GGUGUUGACU GUUGAAUCUC AUGGCAACAC C

2. entity 2

RVRTRGKRRI RRXP

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.8 mM pre-miR21, 0.8 mM ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO, 10 mM potassium phosphate, 10 mM sodium chloride, 10 mM EDTA, 100% D2O.

#	Name	Isotope labeling	Concentration
1	ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO	natural abundance	0.8 mM
2	EDTA	natural abundance	10 mM
3	potassium phosphate	natural abundance	10 mM
4	pre-miR21	natural abundance	0.8 mM
5	sodium chloride	natural abundance	10 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 1 mM ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO, 10 mM potassium phosphate, 10 mM sodium chloride, 95% H2O/5% D2O.

#	Name	Isotope labeling	Concentration
6	ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO	natural abundance	1 mM
7	potassium phosphate	natural abundance	10 mM
8	sodium chloride	natural abundance	10 mM

Chem. Shift Complete2

Sequence coverage: 28.9 %, Completeness: 30.3 %, Completeness (bb): 31.3 % Detail

Polymer type: polyribonucleotide polypeptide(L)

	Total	¹H	¹⁵N
All	30.3 % (242 of 798)	31.1 % (230 of 740)	20.7 % (12 of 58)
Backbone	31.3 % (140 of 448)	30.2 % (128 of 424)	50.0 % (12 of 24)
Sidechain	29.1 % (102 of 350)	32.3 % (102 of 316)	0.0 % (0 of 34)
Aromatic	31.8 % (56 of 176)	39.4 % (56 of 142)	0.0 % (0 of 34)
Methyl	50.0 % (5 of 10)	50.0 % (5 of 10)

1. entity 1

GGUGUUGACU GUUGAAUCUC AUGGCAACAC C

2. entity 2

RVRTRGKRRI RRXP

Show sample condition

Sample #1

#	Name	Isotope labeling	Concentration
1	ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO	natural abundance	0.8 mM
2	EDTA	natural abundance	10 mM
3	potassium phosphate	natural abundance	10 mM
4	pre-miR21	natural abundance	0.8 mM
5	sodium chloride	natural abundance	10 mM

Sample #2

#	Name	Isotope labeling	Concentration
6	ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO	natural abundance	1 mM
7	potassium phosphate	natural abundance	10 mM
8	sodium chloride	natural abundance	10 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 5UZZ, Strand ID: B Detail

Release date

2017-05-24

Citation

A Macrocyclic Peptide Ligand Binds the Oncogenic MicroRNA-21 Precursor and Suppresses Dicer Processing
Shortridge, M.D., Walker, M.J., Pavelitz, T., Chen, Y., Yang, W., Varani, G.
ACS Chem. Biol. (2017), 12, 1611-1620, PubMed 28437065 , DOI 10.1021/acschembio.7b00180 , Abstract

Related entities 1. 14-mer Peptide/RNA Complex, entity 1, : 1 : 1 : 1 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker DRX - 500 MHz with tci cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.8 mM pre-miR21, 0.8 mM ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO, 10 mM potassium phosphate, 10 mM sodium chloride, 10 mM EDTA, 100% D2O.

#	Name	Isotope labeling	Concentration
1	ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO	natural abundance	0.8 mM
2	EDTA	natural abundance	10 mM
3	potassium phosphate	natural abundance	10 mM
4	pre-miR21	natural abundance	0.8 mM
5	sodium chloride	natural abundance	10 mM

2 2D 1H-1H NOESY

Instrument

Bruker DRX - 500 MHz with tci cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO	natural abundance	0.8 mM
2	EDTA	natural abundance	10 mM
3	potassium phosphate	natural abundance	10 mM
4	pre-miR21	natural abundance	0.8 mM
5	sodium chloride	natural abundance	10 mM

3 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 800 MHz with tci cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO	natural abundance	0.8 mM
2	EDTA	natural abundance	10 mM
3	potassium phosphate	natural abundance	10 mM
4	pre-miR21	natural abundance	0.8 mM
5	sodium chloride	natural abundance	10 mM

4 2D 1H-1H TOCSY

Instrument

Bruker DRX - 500 MHz with tci cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 1 mM ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO, 10 mM potassium phosphate, 10 mM sodium chloride, 95% H2O/5% D2O.

#	Name	Isotope labeling	Concentration
6	ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO	natural abundance	1 mM
7	potassium phosphate	natural abundance	10 mM
8	sodium chloride	natural abundance	10 mM

5 2D 1H-1H NOESY

Instrument

Bruker DRX - 500 MHz with tci cryoprobe

Sample

#	Name	Isotope labeling	Concentration
6	ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO	natural abundance	1 mM
7	potassium phosphate	natural abundance	10 mM
8	sodium chloride	natural abundance	10 mM

6 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz with tci cryoprobe

Sample

#	Name	Isotope labeling	Concentration
6	ARG-VAL-ARG-THR-ARG-GLY-LYS-ARG-ARG-ILE-ARG-ARG-DPR-PRO	natural abundance	1 mM
7	potassium phosphate	natural abundance	10 mM
8	sodium chloride	natural abundance	10 mM

NMR combined restraints 9 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30258_5uzz.nef
Input source #2: Coordindates	5uzz.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)
2:12:ARG:C	2:13:DPR:N	unknown	unknown	n/a
2:13:DPR:C	2:14:PRO:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	13	DPR	D-PROLINE	Distance restraints, Coordinates

Sequence alignments

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

-------30--------40--------50--
GGUGUUGACUGUUGAAUCUCAUGGCAACACC
|||||||||||||||||||||||||||||||
GGUGUUGACUGUUGAAUCUCAUGGCAACACC
--------10--------20--------30-

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

--------10----
RVRTRGKRRIRRXP
||||||||||||||
RVRTRGKRRIRRXP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	31	0	0	100.0
B	B	14	0	0	100.0

Content subtype: combined_30258_5uzz.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_chemical_shifts_1	OK	162		100.0 (chain: A, length: 31)
2	Assigned chemical shifts	assigned_chemical_shifts_2	Warning	85		92.9 (chain: B, length: 14)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	31 (1)	noe	78.6 (chain: B, length: 14)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	394 (1)	noe	100.0 (chain: B, length: 14)
3	Distance restraints	CNS/XPLOR_distance_constraints_7	OK	121 (1)	noe	74.2 (chain: A, length: 31)
4	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	11 (1)	hbond	42.9 (chain: B, length: 14)
5	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	7 (1)	hbond	12.9 (chain: A, length: 31)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	Warning	58 (58)	.	29.0 (chain: A, length: 31)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 162
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
Saveframe: assigned_chemical_shifts_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 14, Sequence coverage: 92.9%
- Total number of assignments
  - ¹H chemical shifts: 72
  - ¹⁵N chemical shifts: 13
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
23	G	H21	6.33
25	G	H21	6.51
28	G	H22	7.22
28	G	H21	5.96

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	271	158	58.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	186	102	54.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	85	56	65.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	18	81.8

Comp_index_ID	Comp_ID
13	DPR

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
14	PRO	N	120.419

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	99	71	71.7
¹⁵N chemical shifts	19	12	63.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	25	96.2
¹⁵N chemical shifts	12	12	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	46	63.0
¹⁵N chemical shifts	7	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	5	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: B, Chain length: 14, Sequence coverage: 78.6%
- Total number of restraints: 31
- Weight of restraints: 1.0 (31)
- Potential type of restraints: square-well-parabolic (31)
- Range of distance target values: 2.5, 4.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 14, Sequence coverage: 100.0%
  - Total number of restraints: 394
  - Weight of restraints: 1.0 (394)
  - Potential type of restraints: square-well-parabolic (394)
  - Range of distance target values: 2.5, 5.0 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
      None
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_7
    - Status: OK
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 74.2%
    - Total number of restraints: 121
    - Weight of restraints: 1.0 (121)
    - Potential type of restraints: square-well-parabolic (121)
    - Range of distance target values: 2.5, 5.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_3
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: B, Chain length: 14, Sequence coverage: 42.9%
      - Total number of restraints: 11
        Total hydrogen bond restraints: 11
        O...h-N: 2
        O...H-x: 2
        Long range: 7
        O...h-N: 4
        O...H-x: 3
      - Weight of restraints: 1.0 (11)
        Total hydrogen bond restraints: 1.0 (11)
        O...h-N: 1.0 (2)
        O...H-x: 1.0 (2)
        Long range: 1.0 (7)
        O...h-N: 1.0 (4)
        O...H-x: 1.0 (3)
      - Potential type of restraints: square-well-parabolic (11)
        Total hydrogen bond restraints: square-well-parabolic (11)
        O...h-N: square-well-parabolic (2)
        O...H-x: square-well-parabolic (2)
        Long range: square-well-parabolic (7)
        O...h-N: square-well-parabolic (4)
        O...H-x: square-well-parabolic (3)
      - Range of distance target values: 1.73, 2.73 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
        None
        Chain_ID: B
      - Distance restraints on contact map
      - Saveframe: CNS/XPLOR_distance_constraints_5
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 12.9%
        Total number of restraints: 7
        Total hydrogen bond restraints: 7
        Weight of restraints: 1.0 (7)
        Total hydrogen bond restraints: 1.0 (7)
        Potential type of restraints: square-well-parabolic (7)
        Total hydrogen bond restraints: square-well-parabolic (7)
        Range of distance target values: 1.86, 3.63 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
        None
        Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_6
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 31, Sequence coverage: 29.0%
- Total number of restraints: 58
- Total number of restraints per polymer type: 58
- Weight of restraints: 1.0 (58)
- Potential type of restraints: square-well-parabolic (58)
- Dihedral angle restraints per residue

Keywords TRANSPORT PROTEIN-RNA complex, microRNA miR-21 oncomiR pre-miRNA

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Found 1 Document (0.448 seconds)

BMRB: 30258

Sample #1

Sample #2

Sample #1

Sample #2

Related entities 1. 14-mer Peptide/RNA Complex, entity 1, : 1 : 1 : 1 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 9 contents Detail