BMRB: 6956

RNA recognition by the Vts1 SAM domain

Authors

Donaldson, L.W., Johnson, P.E.

Assembly

PROTEIN/RNA Complex

Entity

1. Vts1p (polymer, Thiol state: not present), 119 monomers, 13079.72 Da Detail

GSNVFNNTIT HPNAGPTSAT STSTSSNGNT PLSSNSSMNP KSLTDPKLLK NIPMWLKSLR LHKYSDALSG TPWIELIYLD DETLEKKGVL ALGARRKLLK AFGIVIDYKE RDLIDRSAY

2. RNA (polymer, Thiol state: not present), 19 monomers, 6149.604 Da Detail

GGAGGCUCUG GCAGCUUUC

Total weight

19229.324 Da

Max. entity weight

13079.72 Da

Source organism

Saccharomyces cerevisiae , Drosophila melanogaster

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 63.0 %, Completeness: 57.2 %, Completeness (bb): 54.7 % Detail

Download

• NMR-STAR v3.1 (partial)
• BMRB/XML (partial)
• CSV
• TSV

Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	57.2 % (961 of 1679)	57.3 % (505 of 881)	56.3 % (373 of 663)	61.5 % (83 of 135)
Backbone	54.7 % (497 of 909)	49.7 % (175 of 352)	54.6 % (243 of 445)	70.5 % (79 of 112)
Sidechain	61.5 % (542 of 882)	62.4 % (330 of 529)	63.0 % (208 of 330)	17.4 % (4 of 23)
Aromatic	28.8 % (49 of 170)	31.8 % (27 of 85)	28.2 % (20 of 71)	14.3 % (2 of 14)
Methyl	78.3 % (108 of 138)	78.3 % (54 of 69)	78.3 % (54 of 69)

1. Vts1p

GSNVFNNTIT HPNAGPTSAT STSTSSNGNT PLSSNSSMNP KSLTDPKLLK NIPMWLKSLR LHKYSDALSG TPWIELIYLD DETLEKKGVL ALGARRKLLK AFGIVIDYKE RDLIDRSAY

2. RNA

GGAGGCUCUG GCAGCUUUC

Show sample condition

Sample

Pressure 1 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	Vts1p	[U-15N; U-13C]		0.2 ~ 0.8 mM
2	RNA			0.2 ~ 0.8 mM
3	sodium phosphate buffer			20 mM
4	sodium chloride			150 mM
5	sodium azide			0.02 %
6	H2O			90 %
7	D2O			10 %

Hide sample codition

Chem. Shift Complete2

Sequence coverage: 23.2 %, Completeness: 37.2 %, Completeness (bb): 36.6 % Detail

Download

• NMR-STAR v3.1 (partial)
• BMRB/XML (partial)
• CSV
• TSV

Polymer type: polypeptide(L) polyribonucleotide

	Total	1H	13C	15N
All	37.2 % (1249 of 3358)	37.4 % (659 of 1762)	36.3 % (482 of 1326)	40.0 % (108 of 270)
Backbone	36.6 % (666 of 1818)	34.5 % (243 of 704)	35.8 % (319 of 890)	46.4 % (104 of 224)
Sidechain	38.8 % (684 of 1764)	39.1 % (414 of 1058)	40.3 % (266 of 660)	8.7 % (4 of 46)
Aromatic	20.9 % (71 of 340)	24.7 % (42 of 170)	19.0 % (27 of 142)	7.1 % (2 of 28)
Methyl	50.0 % (138 of 276)	49.3 % (68 of 138)	50.7 % (70 of 138)

1. Vts1p

GSNVFNNTIT HPNAGPTSAT STSTSSNGNT PLSSNSSMNP KSLTDPKLLK NIPMWLKSLR LHKYSDALSG TPWIELIYLD DETLEKKGVL ALGARRKLLK AFGIVIDYKE RDLIDRSAY

2. RNA

GGAGGCUCUG GCAGCUUUC

Show sample condition

Sample

Pressure 1 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	Vts1p	[U-15N; U-13C]		0.2 ~ 0.8 mM
2	RNA			0.2 ~ 0.8 mM
3	sodium phosphate buffer			20 mM
4	sodium chloride			150 mM
5	sodium azide			0.02 %
6	H2O			90 %
7	D2O			10 %

Hide sample codition

LACS Plot; CA

Referencing offset: -0.47 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	null	0.0
1H	DSS	methyl protons	0.0 ppm	null	null	1.0
15N	DSS	methyl protons	0.0 ppm	null	null	0.0

Hide chemical shift referencing parameters

LACS Plot; CB

Referencing offset: -0.47 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	null	0.0
1H	DSS	methyl protons	0.0 ppm	null	null	1.0
15N	DSS	methyl protons	0.0 ppm	null	null	0.0

Hide chemical shift referencing parameters

LACS Plot; HA

Referencing offset: 0.12 ppm, Outliers: 3 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	null	0.0
1H	DSS	methyl protons	0.0 ppm	null	null	1.0
15N	DSS	methyl protons	0.0 ppm	null	null	0.0

Hide chemical shift referencing parameters

LACS Plot; CO

Referencing offset: 2.99 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	null	0.0
1H	DSS	methyl protons	0.0 ppm	null	null	1.0
15N	DSS	methyl protons	0.0 ppm	null	null	0.0

Hide chemical shift referencing parameters

Protein Blocks Logo

Calculated from 1 models in PDB: 2B6G, Strand ID: A Detail

---

Release date

2006-04-25

Citation

RNA recognition by the Vts1p SAM domain
Johnson, P.E., Donaldson, L.W.
Nat. Struct. Mol. Biol. (2006), 13, 177-178, PubMed 16429155 , DOI 10.1038/nsmb1039 , Abstract

Related entities 1. Vts1p, : 1 : 2 : 11 entities Detail

Related entities 2. RNA, : 1 : 1 : 2 entities Detail

Interaction partners 1. Vts1p, : 7 interactors Detail

Experiments performed 4 experiments Detail