BMRBj - BMREntryMaster

Found 1 Document (0.676 seconds)

BMRB: 34422

6SDY

Solution structure of Staufen1 dsRBD4 - hARF1 SBS dsRNA complex.

Authors

Yadav, D.K., Lukavsky, P.J.

Assembly

Double-stranded RNA-binding protein Staufen homolog 1/RNA Complex

Entity

1. Double-stranded RNA-binding protein Staufen homolog 1/RNA Complex, entity 1 (polymer, Thiol state: not present), 74 monomers, 8376.566 Da Detail

GSHMNPISRL AQIQQAKKEK EPEYTLLTER GLPRRREFVM QVKVGNHTAE GTGTNKKVAK RNAAENMLEI LGFK

2. Double-stranded RNA-binding protein Staufen homolog 1/RNA Complex, entity 2 (polymer, Thiol state: not present), 34 monomers, 10962.45 Da Detail

GGCAGAAGCU GCCUCUUCGG AGGCAGUUUC UGCC

Total weight

19339.016 Da

Max. entity weight

10962.45 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealingna

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.6 %, Completeness (bb): 98.2 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	90.6 % (1297 of 1431)	92.2 % (711 of 771)	90.4 % (507 of 561)	79.8 % (79 of 99)
Backbone	98.2 % (797 of 812)	98.0 % (348 of 355)	98.2 % (379 of 386)	98.6 % (70 of 71)
Sidechain	82.7 % (568 of 687)	87.3 % (363 of 416)	80.7 % (196 of 243)	32.1 % (9 of 28)
Aromatic	55.9 % (105 of 188)	79.8 % (75 of 94)	40.0 % (30 of 75)	0.0 % (0 of 19)
Methyl	98.6 % (73 of 74)	97.3 % (36 of 37)	100.0 % (37 of 37)

1. entity 1

GSHMNPISRL AQIQQAKKEK EPEYTLLTER GLPRRREFVM QVKVGNHTAE GTGTNKKVAK RNAAENMLEI LGFK

2. entity 2

GGCAGAAGCU GCCUCUUCGG AGGCAGUUUC UGCC

Show sample condition

Sample #1

Solvent system 90-95% H20/5-10% D20, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 310 uM [U-15N] Staufen1 dsRBD4, 310 uM Unlabelled hARF1, 90-95% H20/5-10% D20

#	Name	Isotope labeling	Type	Concentration
1	Staufen1 dsRBD4	[U-15N]		310 uM
2	hARF1	Unlabelled		310 uM

Sample #2

Solvent system 90-95% H20/5-10% D20, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1, 90-95% H20/5-10% D20

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

Sample #3

Solvent system 90-95% H20/5-10% D20, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 310 uM Unlabelled hARF1, 90-95% H20/5-10% D20

#	Name	Isotope labeling	Type	Concentration
5	hARF1	Unlabelled		310 uM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 478 uM [U-13C] hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
6	hARF1	[U-13C]		478 uM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 354 uM [U-15N] Staufen1 dsRBD4, 354 uM [U-13C] hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	Staufen1 dsRBD4	[U-15N]		354 uM
8	hARF1	[U-13C]		354 uM

Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 451 uM [U-13C; U-15N] Staufen1 dsRBD4, 451 uM Unlabelled hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
9	Staufen1 dsRBD4	[U-13C; U-15N]		451 uM
10	hARF1	Unlabelled		451 uM

Sample #7

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 310 uM Unlabelled hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
11	hARF1	Unlabelled		310 uM

LACS Plot; CA

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

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.08 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.17 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6SDY, Strand ID: A Detail

Release date

2020-01-06

Citation

Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition
Yadav, D.K., Zigackova, D., Zlobina, M., Klumpler, T., Beaumont, C., Kubickova, M., Vanacova, S., Lukavsky, P.J.
Nucleic Acids Res. (2019), 48, 2091-2106, PubMed 31875226 , DOI 10.1093/nar/gkz1163 , Abstract

Related entities 1. Double-stranded RNA-binding protein Staufen homolog 1/RNA Complex, entity 1, : 1 : 1 : 200 entities Detail

Experiments performed 35 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90-95% H20/5-10% D20, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 310 uM [U-15N] Staufen1 dsRBD4, 310 uM Unlabelled hARF1, 90-95% H20/5-10% D20

#	Name	Isotope labeling	Type	Concentration
1	Staufen1 dsRBD4	[U-15N]		310 uM
2	hARF1	Unlabelled		310 uM

2 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Staufen1 dsRBD4	[U-15N]		310 uM
2	hARF1	Unlabelled		310 uM

3 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 950 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Staufen1 dsRBD4	[U-15N]		310 uM
2	hARF1	Unlabelled		310 uM

4 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90-95% H20/5-10% D20, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 405 uM [U-13C; U-15N] Staufen1 dsRBD4, 405 uM Unlabelled hARF1, 90-95% H20/5-10% D20

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

5 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

6 3D HNCA

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

7 3D HNCO

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

8 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

9 3D HNCACB

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

10 3D HBHA(CO)NH

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

11 3D HcccoNH-TOCSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

12 3D CccoNH-TOCSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

13 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

14 3D 1H-13C NOESY aromatic

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

15 3D 1H-15N NOESY

Instrument

Bruker AVANCE III - 950 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Staufen1 dsRBD4	[U-15N]		310 uM
2	hARF1	Unlabelled		310 uM

16 2D 1H-1H, 13C 2F-filtered NOESY

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 451 uM [U-13C; U-15N] Staufen1 dsRBD4, 451 uM Unlabelled hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
9	Staufen1 dsRBD4	[U-13C; U-15N]		451 uM
10	hARF1	Unlabelled		451 uM

17 3D 13C 1F-filtered 2F-edited HSQC-NOESY

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 451 uM [U-13C; U-15N] Staufen1 dsRBD4, 451 uM Unlabelled hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
9	Staufen1 dsRBD4	[U-13C; U-15N]		451 uM
10	hARF1	Unlabelled		451 uM

18 3D 1H-13C NOESY ribose

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 354 uM [U-15N] Staufen1 dsRBD4, 354 uM [U-13C] hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	Staufen1 dsRBD4	[U-15N]		354 uM
8	hARF1	[U-13C]		354 uM

19 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 90-95% H20/5-10% D20, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 310 uM Unlabelled hARF1, 90-95% H20/5-10% D20

#	Name	Isotope labeling	Type	Concentration
5	hARF1	Unlabelled		310 uM

20 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 90-95% H20/5-10% D20, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 310 uM Unlabelled hARF1, 90-95% H20/5-10% D20

#	Name	Isotope labeling	Type	Concentration
5	hARF1	Unlabelled		310 uM

21 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 478 uM [U-13C] hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
6	hARF1	[U-13C]		478 uM

22 3D HCCH-TOCSY

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 478 uM [U-13C] hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
6	hARF1	[U-13C]		478 uM

23 3D 1H-13C NOESY

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 478 uM [U-13C] hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
6	hARF1	[U-13C]		478 uM

24 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 478 uM [U-13C] hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
6	hARF1	[U-13C]		478 uM

25 2D 1H-1H, 13C 1F-filtered 2F-filtered NOESY

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 451 uM [U-13C; U-15N] Staufen1 dsRBD4, 451 uM Unlabelled hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
9	Staufen1 dsRBD4	[U-13C; U-15N]		451 uM
10	hARF1	Unlabelled		451 uM

26 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 354 uM [U-15N] Staufen1 dsRBD4, 354 uM [U-13C] hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	Staufen1 dsRBD4	[U-15N]		354 uM
8	hARF1	[U-13C]		354 uM

27 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 310 uM Unlabelled hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
11	hARF1	Unlabelled		310 uM

28 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 310 uM Unlabelled hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
11	hARF1	Unlabelled		310 uM

29 3D HCCH-COSY aromatic

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 478 uM [U-13C] hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
6	hARF1	[U-13C]		478 uM

30 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

31 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Staufen1 dsRBD4	[U-13C; U-15N]		405 uM
4	hARF1	Unlabelled		405 uM

32 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 451 uM [U-13C; U-15N] Staufen1 dsRBD4, 451 uM Unlabelled hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
9	Staufen1 dsRBD4	[U-13C; U-15N]		451 uM
10	hARF1	Unlabelled		451 uM

33 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 478 uM [U-13C] hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
6	hARF1	[U-13C]		478 uM

34 2D 1H-13C HSQC ribose

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 354 uM [U-15N] Staufen1 dsRBD4, 354 uM [U-13C] hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	Staufen1 dsRBD4	[U-15N]		354 uM
8	hARF1	[U-13C]		354 uM

35 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5, Details 354 uM [U-15N] Staufen1 dsRBD4, 354 uM [U-13C] hARF1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	Staufen1 dsRBD4	[U-15N]		354 uM
8	hARF1	[U-13C]		354 uM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34422_3.str
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

Content subtype: bmr34422_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1382		100.0 (chain: 1, length: 74), 100.0 (chain: 2, length: 34)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 74, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 34, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 796
  - ¹³C chemical shifts: 506
  - ¹⁵N chemical shifts: 80
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	471	459	97.5
¹³C chemical shifts	334	320	95.8
¹⁵N chemical shifts	86	80	93.0

Keywords NMR structure of RNA-protein complex, RNA binding domain., RNA binding protein, Staufen mediated mRNA decay, Staufen1 protein, dsRBD-dsRNA binding protein

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	151	149	98.7
¹³C chemical shifts	148	142	95.9
¹⁵N chemical shifts	71	69	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	320	310	96.9
¹³C chemical shifts	186	178	95.7
¹⁵N chemical shifts	15	11	73.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	300	257	85.7
¹³C chemical shifts	227	186	81.9
¹⁵N chemical shifts	19	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	204	200	98.0
¹³C chemical shifts	170	168	98.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	96	57	59.4
¹³C chemical shifts	57	18	31.6
¹⁵N chemical shifts	19	0	0.0

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Found 1 Document (0.676 seconds)

BMRB: 34422

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Double-stranded RNA-binding protein Staufen homolog 1/RNA Complex, entity 1, : 1 : 1 : 200 entities Detail

Experiments performed 35 experiments Detail

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