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Found 1 Document (1.527 seconds)

BMRB: 34140

5O1T

Solution structure of the RNA binding domain of Nrd1

Authors

Martinez-Lumbreras, S., Perez-Canadillas, J.M.

Assembly

Protein NRD1

Entity

1. Protein NRD1 (polymer), 179 monomers, 20026.30 Da Detail

SIGAPNTTFG TNNHHLYPDE LNVSNNPHYR PKPVSYDSTL PPDHIKVYSR TLFIGGVPLN MKEWDLANVL KPFAEVQSVI LNNSRKHAFV KVYSRHEAEN VLQNFNKDGA LPLRTRWGVG FGPRDCCDYQ HGYSIIPMHR LTDADKKWSV SAQWGGTSGQ PLVTGIVFEE PDIIVGEGV

Formula weight

20026.3 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

Minimization

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.4 %, Completeness: 82.8 %, Completeness (bb): 78.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.8 % (1727 of 2085)	93.6 % (1013 of 1082)	65.1 % (531 of 816)	97.9 % (183 of 187)
Backbone	78.8 % (824 of 1046)	97.5 % (350 of 359)	59.6 % (311 of 522)	98.8 % (163 of 165)
Sidechain	85.6 % (1030 of 1203)	91.7 % (663 of 723)	75.8 % (347 of 458)	90.9 % (20 of 22)
Aromatic	82.0 % (169 of 206)	93.2 % (96 of 103)	69.7 % (69 of 99)	100.0 % (4 of 4)
Methyl	98.9 % (184 of 186)	100.0 % (93 of 93)	97.8 % (91 of 93)

1. entity 1

SIGAPNTTFG TNNHHLYPDE LNVSNNPHYR PKPVSYDSTL PPDHIKVYSR TLFIGGVPLN MKEWDLANVL KPFAEVQSVI LNNSRKHAFV KVYSRHEAEN VLQNFNKDGA LPLRTRWGVG FGPRDCCDYQ HGYSIIPMHR LTDADKKWSV SAQWGGTSGQ PLVTGIVFEE PDIIVGEGV

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 600 uM [U-100% 13C; U-100% 15N] Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Nrd1	[U-100% 13C; U-100% 15N]	600 uM
3	potassium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 800 uM Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	DTT	natural abundance	1 mM
6	Nrd1	natural abundance	800 uM
7	potassium phosphate	natural abundance	25 mM
8	sodium chloride	natural abundance	25 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 400 uM [U-100% 13C; U-100% 15N] expect for Phe and Leu residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	DTT	natural abundance	1 mM
10	Nrd1	[U-100% 13C; U-100% 15N] expect for Phe and Leu residues	400 uM
11	potassium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	25 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 400 uM [U-100% 13C; U-100% 15N] expect for Ile residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DTT	natural abundance	1 mM
14	Nrd1	[U-100% 13C; U-100% 15N] expect for Ile residues	400 uM
15	potassium phosphate	natural abundance	25 mM
16	sodium chloride	natural abundance	25 mM

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 400 uM [U-100% 13C; U-100% 15N] expect for Arg residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
17	DTT	natural abundance	1 mM
18	Nrd1	[U-100% 13C; U-100% 15N] expect for Arg residues	400 uM
19	potassium phosphate	natural abundance	25 mM
20	sodium chloride	natural abundance	25 mM

LACS Plot; CA

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

Referencing offset: 0.36 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: 0.36 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: 0.06 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5O1T, Strand ID: A Detail

Release date

2017-07-24

Citation

The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition
Franco-Echevarria, E., Gonzalez-Polo, N., Zorrilla, S., Martinez-Lumbreras, S., Santiveri, C.M., Campos-Olivas, R., Sanchez, M., Calvo, O., Gonzalez, B., Perez-Canadillas, J.M.
Nucleic Acids Res. (2017), 45, 10293-10305, PubMed 28973465 , DOI 10.1093/nar/gkx685 , Abstract

Related entities 1. Protein NRD1, : 1 : 6 : 1 : 7 entities Detail

Interaction partners 1. Protein NRD1, : 28 interactors Detail

More details for 28 interactors identified by 7 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 600 uM [U-100% 13C; U-100% 15N] Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Nrd1	[U-100% 13C; U-100% 15N]	600 uM
3	potassium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Nrd1	[U-100% 13C; U-100% 15N]	600 uM
3	potassium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM

3 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Nrd1	[U-100% 13C; U-100% 15N]	600 uM
3	potassium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM

4 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Nrd1	[U-100% 13C; U-100% 15N]	600 uM
3	potassium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Nrd1	[U-100% 13C; U-100% 15N]	600 uM
3	potassium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Nrd1	[U-100% 13C; U-100% 15N]	600 uM
3	potassium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM

7 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 800 uM Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
5	DTT	natural abundance	1 mM
6	Nrd1	natural abundance	800 uM
7	potassium phosphate	natural abundance	25 mM
8	sodium chloride	natural abundance	25 mM

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	1 mM
2	Nrd1	[U-100% 13C; U-100% 15N]	600 uM
3	potassium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM

9 2D 1H-1H NOESY F1filtered

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 400 uM [U-100% 13C; U-100% 15N] expect for Phe and Leu residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	DTT	natural abundance	1 mM
10	Nrd1	[U-100% 13C; U-100% 15N] expect for Phe and Leu residues	400 uM
11	potassium phosphate	natural abundance	25 mM
12	sodium chloride	natural abundance	25 mM

10 2D 1H-1H NOESY F1filtered

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 400 uM [U-100% 13C; U-100% 15N] expect for Ile residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DTT	natural abundance	1 mM
14	Nrd1	[U-100% 13C; U-100% 15N] expect for Ile residues	400 uM
15	potassium phosphate	natural abundance	25 mM
16	sodium chloride	natural abundance	25 mM

11 2D 1H-1H NOESY F1filtered

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 400 uM [U-100% 13C; U-100% 15N] expect for Arg residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
17	DTT	natural abundance	1 mM
18	Nrd1	[U-100% 13C; U-100% 15N] expect for Arg residues	400 uM
19	potassium phosphate	natural abundance	25 mM
20	sodium chloride	natural abundance	25 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34140_5o1t.nef
Input source #2: Coordindates	5o1t.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

290-----300-------310-------320-------330-------340-------350-------360-------370-------380-------39
SIGAPNTTFGTNNHHLYPDELNVSNNPHYRPKPVSYDSTLPPDHIKVYSRTLFIGGVPLNMKEWDLANVLKPFAEVQSVILNNSRKHAFVKVYSRHEAEN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SIGAPNTTFGTNNHHLYPDELNVSNNPHYRPKPVSYDSTLPPDHIKVYSRTLFIGGVPLNMKEWDLANVLKPFAEVQSVILNNSRKHAFVKVYSRHEAEN
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------400-------410-------420-------430-------440-------450-------460--------
VLQNFNKDGALPLRTRWGVGFGPRDCCDYQHGYSIIPMHRLTDADKKWSVSAQWGGTSGQPLVTGIVFEEPDIIVGEGV
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VLQNFNKDGALPLRTRWGVGFGPRDCCDYQHGYSIIPMHRLTDADKKWSVSAQWGGTSGQPLVTGIVFEEPDIIVGEGV
-------110-------120-------130-------140-------150-------160-------170---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	179	0	0	100.0

Content subtype: combined_34140_5o1t.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1652		97.8 (chain: A, length: 179)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3754 (1)	noe	97.2 (chain: A, length: 179)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 179, Sequence coverage: 97.8%
- Total number of assignments
  - ¹H chemical shifts: 1017
  - ¹³C chemical shifts: 453
  - ¹⁵N chemical shifts: 182
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
339	ARG	HH21	7.677
340	THR	HG1	4.826
384	ARG	HH11	7.065
384	ARG	HH12	6.367
384	ARG	HH22	6.688
416	CYS	HG	0.331
423	SER	HG	6.432
438	SER	HG	4.171
446	THR	HG1	5.87

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1082	1008	93.2
¹³C chemical shifts	816	453	55.5
¹⁵N chemical shifts	195	182	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	359	347	96.7
¹³C chemical shifts	358	127	35.5
¹⁵N chemical shifts	165	160	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	723	661	91.4
¹³C chemical shifts	458	326	71.2
¹⁵N chemical shifts	30	22	73.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	95	93	97.9
¹³C chemical shifts	95	90	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	103	98	95.1
¹³C chemical shifts	99	69	69.7
¹⁵N chemical shifts	4	4	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 179, Sequence coverage: 97.2%
- Total number of restraints: 3745
- Weight of restraints: 1.0 (3745)
- Potential type of restraints: upper-bound-parabolic (3745)
- Range of distance target values: 2.36, 6.84 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Nrd1, RNA binding protein, RNA-binding, RRM, transcription non-coding RNAs

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Found 1 Document (1.527 seconds)

BMRB: 34140

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Sample #5

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Protein NRD1, : 1 : 6 : 1 : 7 entities Detail

Interaction partners 1. Protein NRD1, : 28 interactors Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 3 contents Detail