BMRB Entry 25800

Name: Solution structure of Plasmodium falciparum SR1-RRM1 in complex with ACAUCA RNA
Published: 2016-10-06

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PDB ID: 2n7c
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25800
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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:

Solution structure of Plasmodium falciparum SR1-RRM1 in complex with ACAUCA RNA

Deposition date:

2015-09-08

Original release date:

2016-10-06

Authors:

Ganguly, Akshay; Verma, Garima; Bhavesh, Neel Sarovar

Citation:

Citation: Ganguly, Akshay; Verma, Garima; Bhavesh, Neel Sarovar. "The N-terminal RNA Recognition Motif of PfSR1 Confers Semi-specificity for Pyrimidines during RNA Recognition" J. Mol. Biol. ., .-. (2018).
PubMed: 30500338

Assembly members:

Assembly members:
PfSR1-RRM1, polymer, 89 residues, 9997.284 Da.
RNA_(5'-R(*AP*CP*AP*UP*CP*A)-3'), polymer, 6 residues, 1859.203 Da.

Natural source:

Natural source: Common Name: malaria parasite P. falciparum Taxonomy ID: 5833 Superkingdom: Eukaryota Kingdom: not available Genus/species: Plasmodium falciparum

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pet28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PfSR1-RRM1: GSHMVIRESVSRIYVGNLPS HVSSRDVENEFRKYGNILKC DVKKTVSGAAFAFIEFEDAR DAADAIKEKDGCDFEGNKLR VEVPFNARE
RNA_(5'-R(*AP*CP*AP*UP*CP*A)-3'): ACAUCA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	398
15N chemical shifts	84
1H chemical shifts	374

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 (5'-R(APCPAPUPCPA)-3')	2

Entities:

Entity 1, entity_1 89 residues - 9997.284 Da.

G-2, S-1, H0 are from pet28a vector

1

GLY

SER

HIS

MET

VAL

ILE

ARG

GLU

SER

VAL

2

SER

ARG

ILE

TYR

VAL

GLY

ASN

LEU

PRO

SER

3

HIS

VAL

SER

ARG

ASP

VAL

GLU

ASN

GLU

4

PHE

ARG

LYS

TYR

GLY

ASN

ILE

LEU

LYS

CYS

5

ASP

VAL

LYS

THR

VAL

SER

GLY

ALA

6

PHE

ALA

PHE

ILE

GLU

PHE

GLU

ASP

ALA

ARG

7

ASP

ALA

ASP

ALA

ILE

LYS

GLU

LYS

ASP

8

GLY

CYS

ASP

PHE

GLU

GLY

ASN

LYS

LEU

ARG

9

VAL

GLU

VAL

PRO

PHE

ASN

ALA

ARG

GLU

Entity 2, RNA (5'-R(*AP*CP*AP*UP*CP*A)-3') 6 residues - 1859.203 Da.

1

A

C

A

U

C

A

Samples:

sample_H2O: PfSR1-RRM1, [U-100% 13C; U-100% 15N], 0.5 – 1 mM; RNA (5'-R(*AP*CP*AP*UP*CP*A)-3')0.5 – 1 mM; sodium phosphate 25 mM; sodium chloride 100 mM; TCEP 3 mM; H2O 90%; D2O 10%

sample_D2O: PfSR1-RRM1, [U-100% 13C; U-100% 15N], 0.5 – 1 mM; RNA (5'-R(*AP*CP*AP*UP*CP*A)-3')0.5 – 1 mM; sodium phosphate 25 mM; sodium chloride 100 mM; TCEP 3 mM; D2O 100%

sample_conditions_1: ionic strength: 125 mM; pH: 5.9; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_H2O	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_H2O	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_H2O	isotropic	sample_conditions_1
3D HNCACB	sample_H2O	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_H2O	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_H2O	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_H2O	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_D2O	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_D2O	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_D2O	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_D2O	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_H2O	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_D2O	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_H2O	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_D2O	isotropic	sample_conditions_1
2D 13C(F1)-filtered, 13C(F2)-filtered 1H-1H NOESY	sample_D2O	isotropic	sample_conditions_1
2D 13C(F2)-edited 1H-1H NOESY aromatic	sample_D2O	isotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

CARA v1.8.4, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - geometry optimization, structure solution

AMBER v15, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 700 MHz