BMRB Entry 25652

Name: Structure of PTB RRM1(41-163) bound to an RNA stemloop containing a structured loop derived from viral internal ribosomal entry site RNA
Published: 2016-08-08

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PDB ID: 2n3o
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25652
MolProbity Validation Chart

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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: Structure of PTB RRM1(41-163) bound to an RNA stemloop containing a structured loop derived from viral internal ribosomal entry site RNA

Deposition date: 2015-06-08 Original release date: 2016-08-08

Authors: Maris, Christophe; Jayne, Sandrine; Damberger, Fred; Ravindranathan, Sapna; Allain, Frederic

Citation: Maris, Christophe; Jayne, Sandrine; Damberger, Fred; Ravindranathan, Sapna; Allain, Frederic. "C-terminal helix folding upon pyrimidine-rich hairpin binding to PTB RRM1. Implications for PTB function in Encephalomyocarditis virus IRES activity." To be Published ., .-..

Assembly members:
PTBRRM1, polymer, 123 residues, 13375.287 Da.
RNA_(5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3'), polymer, 23 residues, 7308.393 Da.

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

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

Entity Sequences (FASTA):
PTBRRM1: GNDSKKFKGDSRSAGVPSRV IHIRKLPIDVTEGEVISLGL PFGKVTNLLMLKGKNQAFIE MNTEEAANTMVNYYTSVTPV LRGQPIYIQFSNHKELKTDS SPNQARAQAALQAVNSVQSG NLA
RNA_(5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3'): GGGACCUGGUCUUUCCAGGU CCC

Data sets:

assigned_chemical_shifts
RDCs
- RDC_list_1
assigned_chemical_shifts
- protein-chemical-shifts
- RNA-chemical-shifts

Data type	Count
13C chemical shifts	535
15N chemical shifts	119
1H chemical shifts	1013
residual dipolar couplings	70

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PTBRRM1	1
2	RNA (5'-R(GPGPGPAPCPCPUPGPGPUPCPUPUPUPCPCPAPGPGPUPCPCP*C)-3')	2

Entities:

Entity 1, PTBRRM1 123 residues - 13375.287 Da.

1

GLY

ASN

ASP

SER

LYS

PHE

LYS

GLY

ASP

2

SER

ARG

SER

ALA

GLY

VAL

PRO

SER

ARG

VAL

3

ILE

HIS

ILE

ARG

LYS

LEU

PRO

ILE

ASP

VAL

4

THR

GLU

GLY

GLU

VAL

ILE

SER

LEU

GLY

LEU

5

PRO

PHE

GLY

LYS

VAL

THR

ASN

LEU

MET

6

LEU

LYS

GLY

LYS

ASN

GLN

ALA

PHE

ILE

GLU

7

MET

ASN

THR

GLU

ALA

ASN

THR

MET

8

VAL

ASN

TYR

THR

SER

VAL

THR

PRO

VAL

9

LEU

ARG

GLY

GLN

PRO

ILE

TYR

ILE

GLN

PHE

10

SER

ASN

HIS

LYS

GLU

LEU

LYS

THR

ASP

SER

11

SER

PRO

ASN

GLN

ALA

ARG

ALA

GLN

ALA

12

LEU

GLN

ALA

VAL

ASN

SER

VAL

GLN

SER

GLY

13

ASN

LEU

ALA

Entity 2, RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3') 23 residues - 7308.393 Da.

1

G

A

C

U

G

U

2

C

U

C

A

G

U

3

C

Samples:

15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O: PTBRRM1, [U-99% 15N], 1 ± 0.2 mM; RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3') 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; H2O 90%; D2O 10%

13C15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O: PTBRRM1, [U-99% 13C; U-99% 15N], 1 ± 0.2 mM; RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3') 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; H2O 90%; D2O 10%

15N-PTBRRM1-13C-SL23H-RNA-in-D2O: PTBRRM1, [U-99% 15N], 1 ± 0.2 mM; RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3'), [U-99% 13C; U-99% 15N], 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; D2O 100%

15N-PTBRRM1-13C-ribose-labeled-U10U12U14-SL23H-RNA-in-D2O: PTBRRM1, [U-99% 15N], 1 ± 0.2 mM; RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3'), [U-13C; U-15N]-ribose-Ura10,Ura12,Ura14, 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; D2O 100%

15N-PTBRRM1-unlabeled-SL23H-RNA-in-D2O: PTBRRM1, [U-99% 15N], 1 ± 0.2 mM; RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3') 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; D2O 100%

13C15N-PTBRRM1-unlabeled-SL23H-RNA-in-D2O: PTBRRM1, [U-99% 13C; U-99% 15N], 1 ± 0.2 mM; RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3') 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; D2O 100%

15N-PTBRRM1-unlabeled-SL23H-RNA-Pf1-phage-in-H2O: PTBRRM1, [U-99% 15N], 1 ± 0.2 mM; RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3') 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; Pf1 phage 13 mg/mL; H2O 90%; D2O 10%

15N-PTBRRM1-13C15N-SL23H-RNA-Pf1-phage-in-D2O: PTBRRM1, [U-99% 15N], 1 ± 0.2 mM; RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3'), [U-99% 13C; U-99% 15N], 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; Pf1 phage 13 mg/mL; D2O 100%

15N-PTBRRM1-13C15N-SL23H-RNA-Pf1-phage-in-H2O: PTBRRM1, [U-99% 15N], 1 ± 0.2 mM; RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3'), [U-99% 13C; U-99% 15N], 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; Pf1 phage 13 mg/mL; H2O 90%; D2O 10%

15N-PTBRRM1-13C15N-SL23H-RNA-in-H2O: PTBRRM1, [U-99% 15N], 1 ± 0.2 mM; RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3'), [U-99% 13C; U-99% 15N], 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; H2O 90%; D2O 10%

15N-PTBRRM1-13C-ribose-labeled-G9U11U13C15-SL23H-RNA-in-D2O: PTBRRM1, [U-99% 15N], 1 ± 0.2 mM; RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3'), [U-13C; U-15N]-ribose-Cyt9,Ura11,Ura13,Gua15, 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; D2O 100%

15N-PTBRRM1-13C-labeled-CU-SL23H-RNA-in-D2O: PTBRRM1, [U-99% 15N], 1 ± 0.2 mM; RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3'), [U-13C; U-15N]-Ura7,Ura10,Cyt11,Ura12,Ura13,Ura14,Cyt15,Cyt16,Ura20,Cyt21,Cyt22,Cyt23, 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; D2O 100%

13C-SL23H-RNA-in-D2O: RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3'), [U-99% 13C; U-99% 15N], 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; D2O 100%

unlabeled-SL23H-RNA-in-H2O: RNA (5'-R(*GP*GP*GP*AP*CP*CP*UP*GP*GP*UP*CP*UP*UP*UP*CP*CP*AP*GP*GP*UP*CP*CP*C)-3') 1 ± 0.2 mM; sodium phosphate 10 ± 0.1 mM; sodium chloride 20 ± 0.2 mM; H2O 90%; D2O 10%

40C: ionic strength: 0.020 M; pH: 6.5; pressure: 1 atm; temperature: 313 K

25C: ionic strength: 0.020 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

5C: ionic strength: 0.020 M; pH: 6.5; pressure: 1 atm; temperature: 278 K

30C: ionic strength: 0.020 M; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	13C15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	40C
3D HN(CO)CA	13C15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	40C
3D HNCACB	13C15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	40C
3D HNCO	13C15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	40C
3D H(C)CH-TOCSY	13C15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	40C
3D (H)CCH-TOCSY	13C15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	40C
3D 1H-15N NOESY-HSQC	15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	40C
3D 1H-13C NOESY aliphatic-HSQC	13C15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	40C
3D 1H-13C NOESY aromatic-HSQC	13C15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	40C
2D 1H-1H TOCSY	15N-PTBRRM1-unlabeled-SL23H-RNA-in-D2O	isotropic	40C
2D 1H-1H NOESY	15N-PTBRRM1-unlabeled-SL23H-RNA-in-D2O	isotropic	40C
3D f1-13Cfiltered,f2-13C-edited NOESY aliphatic-HSQC	15N-PTBRRM1-13C-SL23H-RNA-in-D2O	isotropic	40C
3D f1-13Cfiltered,f2-13C-edited NOESY aliphatic-HSQC	15N-PTBRRM1-13C-ribose-labeled-U10U12U14-SL23H-RNA-in-D2O	isotropic	40C
2D f2-13C-filtered NOESY	15N-PTBRRM1-13C-SL23H-RNA-in-D2O	isotropic	40C
3D aliphatic-HSQC-NOESY	13C15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	5C
2D H2C2 TROSY	15N-PTBRRM1-13C-SL23H-RNA-in-D2O	isotropic	40C
2D H6C6 TROSY	15N-PTBRRM1-13C-SL23H-RNA-in-D2O	isotropic	40C
2D H8C8 TROSY	15N-PTBRRM1-13C-SL23H-RNA-in-D2O	isotropic	40C
2D H2C2 TROSY	15N-PTBRRM1-13C15N-SL23H-RNA-Pf1-phage-in-D2O	anisotropic	40C
2D H6C6 TROSY	15N-PTBRRM1-13C15N-SL23H-RNA-Pf1-phage-in-D2O	anisotropic	40C
2D H8C8 TROSY	15N-PTBRRM1-13C15N-SL23H-RNA-Pf1-phage-in-D2O	anisotropic	40C
2D H5C5 TROSY	15N-PTBRRM1-13C-SL23H-RNA-in-D2O	isotropic	40C
2D H1'C1' TROSY	15N-PTBRRM1-13C-SL23H-RNA-in-D2O	isotropic	40C
2D H5C5 TROSY	15N-PTBRRM1-13C15N-SL23H-RNA-Pf1-phage-in-D2O	anisotropic	40C
2D H1'C1' TROSY	15N-PTBRRM1-13C15N-SL23H-RNA-Pf1-phage-in-D2O	anisotropic	40C
2D HN TROSY	15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	40C
2D HN TROSY	15N-PTBRRM1-unlabeled-SL23H-RNA-Pf1-phage-in-H2O	anisotropic	40C
2D HN TROSY	15N-PTBRRM1-13C15N-SL23H-RNA-in-H2O	isotropic	5C
2D HN TROSY	15N-PTBRRM1-13C15N-SL23H-RNA-Pf1-phage-in-H2O	anisotropic	5C
2D {1H}15N-NOE HSQC	15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	40C
2D 1H-1H NOESY	15N-PTBRRM1-unlabeled-SL23H-RNA-in-H2O	isotropic	5C
3D f1-13Cfiltered,f2-13C-edited NOESY aliphatic-HSQC	15N-PTBRRM1-13C-labeled-CU-SL23H-RNA-in-D2O	isotropic	40C
3D 1H-13C NOESY aliphatic	15N-PTBRRM1-13C-labeled-CU-SL23H-RNA-in-D2O	isotropic	40C
3D 1H-13C NOESY aliphatic	15N-PTBRRM1-13C-ribose-labeled-U10U12U14-SL23H-RNA-in-D2O	isotropic	40C
3D f1-13Cfiltered,f2-13C-edited NOESY aliphatic-HSQC	15N-PTBRRM1-13C-ribose-labeled-G9U11U13C15-SL23H-RNA-in-D2O	isotropic	40C
2D 1H-13C HSQC aliphatic	15N-PTBRRM1-13C-ribose-labeled-U10U12U14-SL23H-RNA-in-D2O	isotropic	40C
2D 1H-13C HSQC aromatic	15N-PTBRRM1-13C-SL23H-RNA-in-D2O	isotropic	40C
3D 1H-13C NOESY aliphatic	15N-PTBRRM1-13C-SL23H-RNA-in-D2O	isotropic	40C
3D 1H-13C NOESY aromatic	15N-PTBRRM1-unlabeled-SL23H-RNA-in-D2O	isotropic	40C
3D 1H-13C NOESY aliphatic	13C-SL23H-RNA-in-D2O	isotropic	30C
3D 1H-13C NOESY aromatic	13C-SL23H-RNA-in-D2O	isotropic	30C
2D 1H-13C HSQC aliphatic	15N-PTBRRM1-13C-ribose-labeled-G9U11U13C15-SL23H-RNA-in-D2O	isotropic	40C
2D 1H-1H NOESY	unlabeled-SL23H-RNA-in-H2O	isotropic	5C

Software:

SPARKY v3.114, Goddard - chemical shift assignment, peak picking

UNIO/ATNOS-CANDID v10, Herrmann, Guntert and Wuthrich - NOE assignment, peak picking

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - NOE assignment, chemical shift assignment, structure calculation

AMBER v12, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure refinement

ProcheckNMR v3.5.4, Laskowski and MacArthur - validation

Molmol v2K.2, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 600 MHz
Bruker Avance 700 MHz
Bruker Avance 750 MHz
Bruker Avance 900 MHz

Biological Magnetic Resonance Data Bank