BMRB Entry 25052

Name: A structure-based mechanism for tRNA and retroviral RNA remodeling during primer annealing
Published: 2014-09-15

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PDB ID: 2mqv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25052
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: A structure-based mechanism for tRNA and retroviral RNA remodeling during primer annealing PubMed: 25209668

Deposition date: 2015-10-16 Original release date: 2014-09-15

Authors: D'Souza, Victoria; Yildiz, Zehra

Citation: Miller, Sarah; Yildiz, F.; Lo, Jennifer; Wang, Bo; D'Souza, Victoria. "A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing" Nature 515, 591-595 (2014).

Assembly members:
entity_1, polymer, 56 residues, 6377.297 Da.
RNA_(68-MER), polymer, 68 residues, 21894.025 Da.

Natural source: Common Name: Murine Leukemia Virus Taxonomy ID: 11786 Superkingdom: not available Kingdom: not available Genus/species: Gammaretrovirus not available

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: ATVVSGQKQDRQGGERRRSQ LDRDQCAYCKEKGHWAKDCP KKPRGPRGPRPQTSLL
RNA_(68-MER): GGGCGAGGGUCUCCUCUGAG UGAUUGACUACCCGUCAGCG GGGGUCUUUCAUUUGGGGGC UCGUGCCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_1_dup

Data type	Count
1H chemical shifts	252

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	RNA (68-MER)	2

Entities:

Entity 1, entity_1 56 residues - 6377.297 Da.

1

ALA

THR

VAL

SER

GLY

GLN

LYS

GLN

ASP

2

ARG

GLN

GLY

GLU

ARG

SER

GLN

3

LEU

ASP

ARG

ASP

GLN

CYS

ALA

TYR

CYS

LYS

4

GLU

LYS

GLY

HIS

TRP

ALA

LYS

ASP

CYS

PRO

5

LYS

PRO

ARG

GLY

PRO

ARG

GLY

PRO

ARG

6

PRO

GLN

THR

SER

LEU

Entity 2, RNA (68-MER) 68 residues - 21894.025 Da.

1

G

C

G

A

G

U

2

C

U

C

U

C

U

G

A

G

3

U

G

A

U

G

A

C

U

A

4

C

G

U

C

A

G

C

G

5

G

U

C

U

C

6

A

U

G

C

7

U

C

G

U

G

C

Samples:

sample_1-U5-PBS: U5-PBS-NC, 15N,13C-Alab, 0.5 mM; U5-PBS-NC, 15N,13C-Glab, 0.5 mM; U5-PBS-NC, 15N,13C-Ulab, 0.5 mM; U5-PBS-NC, 15N,13C-Clab, 0.5 mM; NaCl 10 mM; Tris 10 mM; H2O 90%; D2O 10%

sample_2-U5-PBS-M2: U5-PBS-M2-NC 0.5 mM; NaCl 10 mM; Tris 10 mM; D2O 100%

sample_3-linker: UAUCG-linker 1 mM; NaCl 10 mM; Tris 10 mM; D2O 100%

sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 311 K

sample_conditions_2: pH: 7.0; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1-U5-PBS	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1-U5-PBS	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2-U5-PBS-M2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3-linker	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_1-U5-PBS	isotropic	sample_conditions_1

Software:

CYANA, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax, Guntert, Mumenthaler and Wuthrich, Johnson, One Moon Scientific - data analysis, processing, refinement

NMR spectrometers:

Bruker DMX 700 MHz

BMRB	25100 25101
PDB	1A6B 1U6P 1WWD 1WWE 1WWF 1WWG 2MQV 2MS0 2MS1
GB	AAB59942 AAB64159 AAC82566 AAC82568 AAL69908
PRF	0711245A
REF	NP_057933 NP_057934 NP_955586
SP	P03332 P03355 Q8UN02

Biological Magnetic Resonance Data Bank