BMRB Entry 17504

Name: RNA Duplex-Quadruplex Junction Complex with FMRP RGG peptide
Published: 2011-06-07

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PDB ID: 2la5
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR17504
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: RNA Duplex-Quadruplex Junction Complex with FMRP RGG peptide PubMed: 21642970

Deposition date: 2011-03-03 Original release date: 2011-06-07

Authors: Phan, Anh Tuan; Kuryavyi, Vitaly V; Darnell, Jennifer C; Serganov, Alexander; Majumdar, Ananya; Ilin, Serge; Darnell, Robert B; Patel, Dinshaw J

Citation: Phan, Anh Tuan; Kuryavyi, Vitaly; Darnell, Jennifer; Serganov, Alexander; Majumdar, Ananya; Ilin, Serge; Raslin, Tanya; Polonskaia, Anna; Chen, Cynthia; Clain, David; Darnell, Robert; Patel, Dinshaw. "Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction." Nat. Struct. Mol. Biol. 18, 796-804 (2011).

Assembly members:
RNA_(36-MER), polymer, 36 residues, 11805.102 Da.
entity_2, polymer, 17 residues, 1757.934 Da.

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):
RNA_(36-MER): GCUGCGGUGUGGAAGGAGUG GCUGGGUUGCGCAGCG
entity_2: GPRRGDGRRRGGGGRGQ

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	410

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (36-MER)	1
2	entity_2	2

Entities:

Entity 1, RNA (36-MER) 36 residues - 11805.102 Da.

1

G

C

U

G

C

G

U

G

U

2

G

A

G

A

G

U

G

3

G

C

U

G

U

G

C

4

G

C

A

G

C

G

Entity 2, entity_2 17 residues - 1757.934 Da.

1

GLY

PRO

ARG

GLY

ASP

GLY

ARG

2

GLY

ARG

GLY

GLN

Samples:

sample_1: RNA (36-MER) 1 mM; Peptide 1 mM

sample_2: RNA (36-MER), [U-100% 13C; U-100% 15N], 0.5 mM; Peptide 0.5 mM

sample_3: RNA (36-MER) 0.5 mM; Peptide, [U-100% 13C; U-100% 15N], 0.5 mM

sample_4: RNA (36-MER), [U-100% 13C; U-100% 15N], 0.2-0.5 mM; Peptide, [U-100% 13C; U-100% 15N], 0.2-0.5 mM

sample_5: RNA (36-MER), [U-13C; U-15N]-Gua, 0.5 mM; Peptide 0.5 mM

sample_6: RNA (36-MER), [U-13C; U-15N]-Ade, 0.2 mM; Peptide 0.2 mM

sample_7: RNA (36-MER), [U-13C; U-15N]-Cyt, 0.2 mM; Peptide 0.2 mM

sample_8: RNA (36-MER), [U-13C; U-15N]-Ura, 0.2 mM; Peptide 0.2 mM

sample_9: RNA (36-MER), rG-to-dG and rU-to-dU 2% 15N-labelled, 0.2 mM; Peptide 0.2 mM

sample_conditions_1: ionic strength: 0.050 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
JR	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 13C-1H CTHSQC	sample_2	isotropic	sample_conditions_1
HNH-COSY	sample_2	isotropic	sample_conditions_1
HNN-COSY	sample_2	isotropic	sample_conditions_1
HCCH-COSY	sample_2	isotropic	sample_conditions_1
HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
13C-edited NOESY	sample_2	isotropic	sample_conditions_1
15N-edited NOESY	sample_2	isotropic	sample_conditions_1
15N-1H HSQC	sample_3	isotropic	sample_conditions_1
13C-1H HSQC	sample_3	isotropic	sample_conditions_1
HNCA	sample_3	isotropic	sample_conditions_1
HNCO	sample_3	isotropic	sample_conditions_1
HNCOCA	sample_3	isotropic	sample_conditions_1
HNCACB	sample_3	isotropic	sample_conditions_1
HBHACONH	sample_3	isotropic	sample_conditions_1
HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
HCCH-COSY	sample_3	isotropic	sample_conditions_1
13C-edited NOESY	sample_3	isotropic	sample_conditions_1
15N-edited NOESY	sample_3	isotropic	sample_conditions_1
HNN-COSY	sample_4	isotropic	sample_conditions_1
13C-edited NOESY	sample_4	isotropic	sample_conditions_1
15N-edited NOESY	sample_4	isotropic	sample_conditions_1
CTHSQC	sample_5	isotropic	sample_conditions_1
HCCH-COSY	sample_5	isotropic	sample_conditions_1
HCCH-TOCSY	sample_5	isotropic	sample_conditions_1
13C-edited NOESY	sample_5	isotropic	sample_conditions_1
CTHSQC	sample_6	isotropic	sample_conditions_1
HCCH-COSY	sample_6	isotropic	sample_conditions_1
HCCH-TOCSY	sample_6	isotropic	sample_conditions_1
13C-edited NOESY	sample_6	isotropic	sample_conditions_1
CTHSQC	sample_7	isotropic	sample_conditions_1
HCCH-COSY	sample_7	isotropic	sample_conditions_1
HCCH-TOCSY	sample_7	isotropic	sample_conditions_1
13C-edited NOESY	sample_7	isotropic	sample_conditions_1
CTHSQC	sample_8	isotropic	sample_conditions_1
HCCH-COSY	sample_8	isotropic	sample_conditions_1
HCCH-TOCSY	sample_8	isotropic	sample_conditions_1
13C-edited NOESY	sample_8	isotropic	sample_conditions_1
1D 15N-filtered	sample_9	isotropic	sample_conditions_1
2D NOESY	sample_9	isotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

AMBER, Accelrys Software Inc. - geometry optimization

FELIX, Accelrys Software Inc. - processing

VNMR, Varian - collection

TOPSPIN, Bruker Biospin - collection

CARA, K. Wuthrich - data analysis

NMR spectrometers:

Varian Unity 600 MHz
Bruker Avance 600 MHz
Bruker Avance 700 MHz
Bruker Avance 800 MHz