BMRBj - BMREntryMaster

Found 1 Document (0.771 seconds)

BMRB: 25042

2MQP

Structural Investigation of hnRNP L bound to RNA

Authors

Blatter, M., Allain, F.

Assembly

Second RNA Recognition Motif Domain of hnRNP L bound to ACACAC RNA

Entity

1. Second RNA Recognition Motif Domain of hnRNP L bound to ACACAC RNA, entity 1 (polymer, Thiol state: all free), 118 monomers, 13067.60 Da Detail

QKISRPGDSD DSRSVNSVLL FTILNPIYSI TTDVLYTICN PCGPVQRIVI FRKNGVQAMV EFDSVQSAQR AKASLNGADI YSGCCTLKIE YAKPTRLNVF KNDQDTWDYT NPNLSGQG

2. RNA (5'-R(*AP*CP*AP*CP*AP*C)-3') (polymer, Thiol state: all free), 6 monomers, 1921.178 Da Detail

ACACAC

Total weight

14988.777 Da

Max. entity weight

13067.6 Da

Source organism

Rattus norvegicus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 95.2 %, Completeness: 83.0 %, Completeness (bb): 75.7 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	83.0 % (1202 of 1449)	90.7 % (686 of 756)	68.8 % (388 of 564)	99.2 % (128 of 129)
Backbone	75.7 % (577 of 762)	85.3 % (233 of 273)	61.5 % (232 of 377)	100.0 % (112 of 112)
Sidechain	92.2 % (736 of 798)	93.8 % (453 of 483)	89.6 % (267 of 298)	94.1 % (16 of 17)
Aromatic	61.2 % (71 of 116)	75.9 % (44 of 58)	45.6 % (26 of 57)	100.0 % (1 of 1)
Methyl	100.0 % (132 of 132)	100.0 % (66 of 66)	100.0 % (66 of 66)

1. entity 1

QKISRPGDSD DSRSVNSVLL FTILNPIYSI TTDVLYTICN PCGPVQRIVI FRKNGVQAMV EFDSVQSAQR AKASLNGADI YSGCCTLKIE YAKPTRLNVF KNDQDTWDYT NPNLSGQG

2. RNA (5'-R(*AP*CP*AP*CP*AP*C)-3')

ACACAC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	hnRNP L	[U-100% 15N]	2 mM
2	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
3	sodium chloride	natural abundance	60 mM
4	sodium phosphate	natural abundance	40 mM
5	DTT	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	hnRNP L	[U-100% 13C; U-100% 15N]	2 mM
9	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
10	sodium chloride	natural abundance	60 mM
11	sodium phosphate	natural abundance	40 mM
12	DTT	natural abundance	1 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	hnRNP L	[U-100% 15N]	2 mM
16	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
17	sodium chloride	natural abundance	60 mM
18	sodium phosphate	natural abundance	40 mM
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	hnRNP L	[U-100% 13C; U-100% 15N]	2 mM
22	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
23	sodium chloride	natural abundance	60 mM
24	sodium phosphate	natural abundance	40 mM
25	DTT	natural abundance	1 mM
26	D2O	natural abundance	100 %

Chem. Shift Complete2

Sequence coverage: 26.6 %, Completeness: 53.0 %, Completeness (bb): 50.3 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	53.0 % (1535 of 2898)	57.3 % (867 of 1512)	45.2 % (510 of 1128)	61.2 % (158 of 258)
Backbone	50.3 % (767 of 1524)	57.7 % (315 of 546)	41.8 % (315 of 754)	61.2 % (137 of 224)
Sidechain	56.2 % (897 of 1596)	57.1 % (552 of 966)	54.4 % (324 of 596)	61.8 % (21 of 34)
Aromatic	47.8 % (111 of 232)	55.2 % (64 of 116)	40.4 % (46 of 114)	50.0 % (1 of 2)
Methyl	57.2 % (151 of 264)	57.6 % (76 of 132)	56.8 % (75 of 132)

1. entity 1

QKISRPGDSD DSRSVNSVLL FTILNPIYSI TTDVLYTICN PCGPVQRIVI FRKNGVQAMV EFDSVQSAQR AKASLNGADI YSGCCTLKIE YAKPTRLNVF KNDQDTWDYT NPNLSGQG

2. RNA (5'-R(*AP*CP*AP*CP*AP*C)-3')

ACACAC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	hnRNP L	[U-100% 15N]	2 mM
2	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
3	sodium chloride	natural abundance	60 mM
4	sodium phosphate	natural abundance	40 mM
5	DTT	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	hnRNP L	[U-100% 13C; U-100% 15N]	2 mM
9	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
10	sodium chloride	natural abundance	60 mM
11	sodium phosphate	natural abundance	40 mM
12	DTT	natural abundance	1 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	hnRNP L	[U-100% 15N]	2 mM
16	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
17	sodium chloride	natural abundance	60 mM
18	sodium phosphate	natural abundance	40 mM
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	hnRNP L	[U-100% 13C; U-100% 15N]	2 mM
22	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
23	sodium chloride	natural abundance	60 mM
24	sodium phosphate	natural abundance	40 mM
25	DTT	natural abundance	1 mM
26	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.11 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MQP, Strand ID: A Detail

Release date

2015-12-20

Related entities 1. Second RNA Recognition Motif Domain of hnRNP L bound to ACACAC RNA, entity 1, : 1 : 7 : 94 entities Detail

Experiments performed 7 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	hnRNP L	[U-100% 15N]	2 mM
2	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
3	sodium chloride	natural abundance	60 mM
4	sodium phosphate	natural abundance	40 mM
5	DTT	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	hnRNP L	[U-100% 13C; U-100% 15N]	2 mM
9	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
10	sodium chloride	natural abundance	60 mM
11	sodium phosphate	natural abundance	40 mM
12	DTT	natural abundance	1 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

3 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	hnRNP L	[U-100% 13C; U-100% 15N]	2 mM
9	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
10	sodium chloride	natural abundance	60 mM
11	sodium phosphate	natural abundance	40 mM
12	DTT	natural abundance	1 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	hnRNP L	[U-100% 15N]	2 mM
16	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
17	sodium chloride	natural abundance	60 mM
18	sodium phosphate	natural abundance	40 mM
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	hnRNP L	[U-100% 15N]	2 mM
16	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
17	sodium chloride	natural abundance	60 mM
18	sodium phosphate	natural abundance	40 mM
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

6 3D F3-filtered-F2-edited NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	hnRNP L	[U-100% 13C; U-100% 15N]	2 mM
22	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
23	sodium chloride	natural abundance	60 mM
24	sodium phosphate	natural abundance	40 mM
25	DTT	natural abundance	1 mM
26	D2O	natural abundance	100 %

7 2D F2-filtered NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	hnRNP L	[U-100% 13C; U-100% 15N]	2 mM
22	RNA (5'-R(APCPAPCPAPC)-3')	natural abundance	2 mM
23	sodium chloride	natural abundance	60 mM
24	sodium phosphate	natural abundance	40 mM
25	DTT	natural abundance	1 mM
26	D2O	natural abundance	100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25042_2mqp.nef
Input source #2: Coordindates	2mqp.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

----180-------190-------200-------210-------220-------230-------240-------250-------260-------270---
QKISRPGDSDDSRSVNSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKNGVQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKPTRLNVF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QKISRPGDSDDSRSVNSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKNGVQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKPTRLNVF
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----280-------290-
KNDQDTWDYTNPNLSGQG
||||||||||||||||||
KNDQDTWDYTNPNLSGQG
-------110--------

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

------
ACACAC
||||||
ACACAC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	118	0	0	100.0
B	B	6	0	0	100.0

Content subtype: combined_25042_2mqp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1214		100.0 (chain: A, length: 118)
2	Assigned chemical shifts	assigned_chem_shift_list_2	OK	77		100.0 (chain: B, length: 6)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	5806 (1)	noe	98.3 (chain: A, length: 118), 66.7 (chain: B, length: 6)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	172 (1)	hbond	45.8 (chain: A, length: 118), 50.0 (chain: B, length: 6)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	Warning	38 (38)	.	27.1 (chain: A, length: 118), 66.7 (chain: B, length: 6)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 118, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 697
  - ¹³C chemical shifts: 383
  - ¹⁵N chemical shifts: 134
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
Saveframe: assigned_chem_shift_list_2
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 41
  - ¹³C chemical shifts: 36
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
225	ARG	HH11	7.071
225	ARG	HH12	7.071
225	ARG	NH1	71.533

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	702	695	99.0
¹³C chemical shifts	522	383	73.4
¹⁵N chemical shifts	135	133	98.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	237	234	98.7
¹³C chemical shifts	236	116	49.2
¹⁵N chemical shifts	112	111	99.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	465	461	99.1
¹³C chemical shifts	286	267	93.4
¹⁵N chemical shifts	23	22	95.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	67	100.0
¹³C chemical shifts	67	67	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	44	95.7
¹³C chemical shifts	45	26	57.8
¹⁵N chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	41	75.9
¹³C chemical shifts	42	36	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	29	80.6
¹³C chemical shifts	30	24	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	12	66.7
¹³C chemical shifts	12	12	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0
¹³C chemical shifts	6	6	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 118, Sequence coverage: 98.3%
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 66.7%
- Total number of restraints: 5767
- Weight of restraints: 1.0 (5767)
- Potential type of restraints: upper-bound-parabolic (5767)
- Range of distance target values: 3.5, 6.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 118, Sequence coverage: 45.8%
    - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 50.0%
  - Total number of restraints: 172
  - Weight of restraints: 1.0 (172)
  - Potential type of restraints: upper-bound-parabolic (172)
  - Range of distance target values: 1.8, 3.4 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 118, Sequence coverage: 27.1%
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 66.7%
- Total number of restraints: 38
- Total number of restraints per polymer type: 38
- Weight of restraints: 1.0 (38)
- Potential type of restraints: square-well-parabolic (38)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: B

Keywords Protein/RNA Complex, RRM

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Found 1 Document (0.771 seconds)

BMRB: 25042

Sample #1

Sample #2

Sample #3

Sample #4

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Second RNA Recognition Motif Domain of hnRNP L bound to ACACAC RNA, entity 1, : 1 : 7 : 94 entities Detail

Experiments performed 7 experiments Detail

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NMR combined restraints 6 contents Detail