BMRB Entry 34385

Name: Solution Structure of ribosome-binding factor A (RbfA) under physiological conditions
Published: 2020-05-29

Click here to enlarge.

PDB ID: 7afr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34385
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

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

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title: Solution Structure of ribosome-binding factor A (RbfA) under physiological conditions PubMed: 34088665

Deposition date: 2019-04-01 Original release date: 2020-05-29

Authors: Schedlbauer, A.; Ochoa Lizarralde, B.; Capuni, R.; Iturrioz, I.; Fucini, P.; Connell, S.

Citation: Schedlbauer, Andreas; Iturrioz, Idoia; Ochoa-Lizarralde, Borja; Diercks, Tammo; Lopez-Alonso, Jorge Pedro; Lavin, Jose Luis; Kaminishi, Tatsuya; Capuni, Retina; Dhimole, Neha; de Astigarraga, Elisa; Gil-Carton, David; Fucini, Paola; Connell, Sean. "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit" Sci. Adv. 7, eabf7547-eabf7547 (2021).

Assembly members:
entity_1, polymer, 140 residues, 15933.329 Da.

Natural source: Common Name: Enterobacter sp. EC-NT1 Taxonomy ID: 2163603 Superkingdom: Bacteria Kingdom: not available Genus/species: Enterobacter Enterobacter sp. EC-NT1

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

Entity Sequences (FASTA):
entity_1: SAKEFGRPQRVAQEMQKEIA LILQREIKDPRLGMMTTVSG VEMSRDLAYAKVYVTFLNDK DEDAVKAGIKALQEASGFIR SLLGKAMRLRIVPELTFFYD NSLVEGMRMSNLVTSVVKHD EERRVNPDDSKEDALEVLFQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	522
15N chemical shifts	114
1H chemical shifts	836

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 140 residues - 15933.329 Da.

1	SER	ALA	LYS	GLU	PHE	GLY	ARG	PRO	GLN	ARG
2	VAL	ALA	GLN	GLU	MET	GLN	LYS	GLU	ILE	ALA
3	LEU	ILE	LEU	GLN	ARG	GLU	ILE	LYS	ASP	PRO
4	ARG	LEU	GLY	MET	MET	THR	THR	VAL	SER	GLY
5	VAL	GLU	MET	SER	ARG	ASP	LEU	ALA	TYR	ALA
6	LYS	VAL	TYR	VAL	THR	PHE	LEU	ASN	ASP	LYS
7	ASP	GLU	ASP	ALA	VAL	LYS	ALA	GLY	ILE	LYS
8	ALA	LEU	GLN	GLU	ALA	SER	GLY	PHE	ILE	ARG
9	SER	LEU	LEU	GLY	LYS	ALA	MET	ARG	LEU	ARG
10	ILE	VAL	PRO	GLU	LEU	THR	PHE	PHE	TYR	ASP
11	ASN	SER	LEU	VAL	GLU	GLY	MET	ARG	MET	SER
12	ASN	LEU	VAL	THR	SER	VAL	VAL	LYS	HIS	ASP
13	GLU	GLU	ARG	ARG	VAL	ASN	PRO	ASP	ASP	SER
14	LYS	GLU	ASP	ALA	LEU	GLU	VAL	LEU	PHE	GLN

Samples:

sample_1: RbfA, [U-98% 13C; U-98% 15N], 400 uM; HEPES 10 mM; MgCl2 6 mM; NH4Cl 30 mM; TCEP 75 uM

sample_conditions_1: ionic strength: 40 mM; pH: 7.6; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCAHA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HNH NOESY	sample_1	isotropic	sample_conditions_1
3D CNH NOESY	sample_1	isotropic	sample_conditions_1
3D HN(CO)CAHA	sample_1	isotropic	sample_conditions_1
3D HCH NOESY	sample_1	isotropic	sample_conditions_1

Software:

Xplor-NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

Sparky, Goddard - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE III 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts

1	SER	ALA	LYS	GLU	PHE	GLY	ARG	PRO	GLN	ARG
2	VAL	ALA	GLN	GLU	MET	GLN	LYS	GLU	ILE	ALA
3	LEU	ILE	LEU	GLN	ARG	GLU	ILE	LYS	ASP	PRO
4	ARG	LEU	GLY	MET	MET	THR	THR	VAL	SER	GLY
5	VAL	GLU	MET	SER	ARG	ASP	LEU	ALA	TYR	ALA
6	LYS	VAL	TYR	VAL	THR	PHE	LEU	ASN	ASP	LYS
7	ASP	GLU	ASP	ALA	VAL	LYS	ALA	GLY	ILE	LYS
8	ALA	LEU	GLN	GLU	ALA	SER	GLY	PHE	ILE	ARG
9	SER	LEU	LEU	GLY	LYS	ALA	MET	ARG	LEU	ARG
10	ILE	VAL	PRO	GLU	LEU	THR	PHE	PHE	TYR	ASP
11	ASN	SER	LEU	VAL	GLU	GLY	MET	ARG	MET	SER
12	ASN	LEU	VAL	THR	SER	VAL	VAL	LYS	HIS	ASP
13	GLU	GLU	ARG	ARG	VAL	ASN	PRO	ASP	ASP	SER
14	LYS	GLU	ASP	ALA	LEU	GLU	VAL	LEU	PHE	GLN

1	SER	ALA	LYS	GLU	PHE	GLY	ARG	PRO	GLN	ARG
2	VAL	ALA	GLN	GLU	MET	GLN	LYS	GLU	ILE	ALA
3	LEU	ILE	LEU	GLN	ARG	GLU	ILE	LYS	ASP	PRO
4	ARG	LEU	GLY	MET	MET	THR	THR	VAL	SER	GLY
5	VAL	GLU	MET	SER	ARG	ASP	LEU	ALA	TYR	ALA
6	LYS	VAL	TYR	VAL	THR	PHE	LEU	ASN	ASP	LYS
7	ASP	GLU	ASP	ALA	VAL	LYS	ALA	GLY	ILE	LYS
8	ALA	LEU	GLN	GLU	ALA	SER	GLY	PHE	ILE	ARG
9	SER	LEU	LEU	GLY	LYS	ALA	MET	ARG	LEU	ARG
10	ILE	VAL	PRO	GLU	LEU	THR	PHE	PHE	TYR	ASP
11	ASN	SER	LEU	VAL	GLU	GLY	MET	ARG	MET	SER
12	ASN	LEU	VAL	THR	SER	VAL	VAL	LYS	HIS	ASP
13	GLU	GLU	ARG	ARG	VAL	ASN	PRO	ASP	ASP	SER
14	LYS	GLU	ASP	ALA	LEU	GLU	VAL	LEU	PHE	GLN

1	SER	ALA	LYS	GLU	PHE	GLY	ARG	PRO	GLN	ARG
2	VAL	ALA	GLN	GLU	MET	GLN	LYS	GLU	ILE	ALA
3	LEU	ILE	LEU	GLN	ARG	GLU	ILE	LYS	ASP	PRO
4	ARG	LEU	GLY	MET	MET	THR	THR	VAL	SER	GLY
5	VAL	GLU	MET	SER	ARG	ASP	LEU	ALA	TYR	ALA
6	LYS	VAL	TYR	VAL	THR	PHE	LEU	ASN	ASP	LYS
7	ASP	GLU	ASP	ALA	VAL	LYS	ALA	GLY	ILE	LYS
8	ALA	LEU	GLN	GLU	ALA	SER	GLY	PHE	ILE	ARG
9	SER	LEU	LEU	GLY	LYS	ALA	MET	ARG	LEU	ARG
10	ILE	VAL	PRO	GLU	LEU	THR	PHE	PHE	TYR	ASP
11	ASN	SER	LEU	VAL	GLU	GLY	MET	ARG	MET	SER
12	ASN	LEU	VAL	THR	SER	VAL	VAL	LYS	HIS	ASP
13	GLU	GLU	ARG	ARG	VAL	ASN	PRO	ASP	ASP	SER
14	LYS	GLU	ASP	ALA	LEU	GLU	VAL	LEU	PHE	GLN