BMRB Entry 6956

Name: RNA recognition by the Vts1 SAM domain
Published: 2006-04-26

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PDB ID: 2b6g
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR6956
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

RNA recognition by the Vts1 SAM domain

Deposition date:

2006-01-27

Original release date:

2006-04-26

Authors:

Donaldson, L.; Johnson, P.

Citation:

Citation: Johnson, P.; Donaldson, L.. "RNA recognition by the Vts1p SAM domain" Nat. Struct. Mol. Biol. 13, 177-178 (2006).
PubMed: 16429155

Assembly members:

Assembly members:
Vts1p, polymer, 119 residues, Formula weight is not available
RNA, polymer, 19 residues, Formula weight is not available

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Vts1p: GSNVFNNTITHPNAGPTSAT STSTSSNGNTPLSSNSSMNP KSLTDPKLLKNIPMWLKSLR LHKYSDALSGTPWIELIYLD DETLEKKGVLALGARRKLLK AFGIVIDYKERDLIDRSAY
RNA: GGAGGCUCUGGCAGCUUUC

Data sets:

assigned_chemical_shifts
- chemical_shift_set_1
- chemical_shift_set_2

Data type	Count
13C chemical shifts	352
15N chemical shifts	83
1H chemical shifts	613

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Vts1p	1
2	5'-R(GPGPAPGPGPCPUPCPUPGPGPCPAPGPCPUPUPUP*C)-3'	2

Entities:

Entity 1, Vts1p 119 residues - Formula weight is not available

1

GLY

SER

ASN

VAL

PHE

ASN

THR

ILE

THR

2

HIS

PRO

ASN

ALA

GLY

PRO

THR

SER

ALA

THR

3

SER

THR

SER

THR

SER

ASN

GLY

ASN

THR

4

PRO

LEU

SER

ASN

SER

MET

ASN

PRO

5

LYS

SER

LEU

THR

ASP

PRO

LYS

LEU

LYS

6

ASN

ILE

PRO

MET

TRP

LEU

LYS

SER

LEU

ARG

7

LEU

HIS

LYS

TYR

SER

ASP

ALA

LEU

SER

GLY

8

THR

PRO

TRP

ILE

GLU

LEU

ILE

TYR

LEU

ASP

9

ASP

GLU

THR

LEU

GLU

LYS

GLY

VAL

LEU

10

ALA

LEU

GLY

ALA

ARG

LYS

LEU

LYS

11

ALA

PHE

GLY

ILE

VAL

ILE

ASP

TYR

LYS

GLU

12

ARG

ASP

LEU

ILE

ASP

ARG

SER

ALA

TYR

Entity 2, 5'-R(*GP*GP*AP*GP*GP*CP*UP*CP*UP*GP*GP*CP*AP*GP*CP*UP*UP*UP*C)-3' 19 residues - Formula weight is not available

1

G

A

G

C

U

C

U

G

2

G

C

A

G

C

U

C

Samples:

sample_1: Vts1p, [U-15N; U-13C], 0.2 – 0.8 mM; RNA0.2 – 0.8 mM; sodium phosphate buffer 20 mM; sodium chloride 150 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_cond_1: ionic strength: 150 mM; pH: 7.8; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 13C-separated NOESY	sample_1	not available	sample_cond_1
3D 15N-separated NOESY	sample_1	not available	sample_cond_1
2D NOESY	sample_1	not available	sample_cond_1
2D 12C-filtered 13C-edited NOESY	sample_1	not available	sample_cond_1

Software:

CYANA v2.1 - structure solution

X-PLOR NIH v2.11.0 - refinement, structure solution

NMR spectrometers:

Varian INOVA 500 MHz

BMRB	6922
PDB	2B6G 2D3D 2F8K 2FE9
DBJ	GAA26663
EMBL	CAA99688
GB	AHY77628 EDN63679 EDV10919 EDZ69055 EEU07517
REF	NP_015004
SP	Q08831
TPG	DAA11120
AlphaFold	Q08831