BMRBj - BMREntryMaster

Found 1 Document (1.268 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)
B:12:ARG:C	B:13:DPR:N	unknown	unknown	n/a
B:13:DPR:C	B: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	nef_chemical_shift_list_assigned_chemical_shifts_1	OK	162		100.0 (chain: A, length: 31)
2	Assigned chemical shifts	nef_chemical_shift_list_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: nef_chemical_shift_list_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: nef_chemical_shift_list_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	Atom_ID	CS value (ppm)
14	PRO	N	120.419

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	106	72	67.9
¹⁵N chemical shifts	12	12	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	26	96.3
¹⁵N chemical shifts	12	12	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	79	46	58.2

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

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 (1.268 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