BMRB Entry 7088

Name: dynamics within the fMet-tRNA binding domain of translation initiation factor IF2 from Bacillus stearothermophilus
Published: 2006-11-21

Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR7088

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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:

dynamics within the fMet-tRNA binding domain of translation initiation factor IF2 from Bacillus stearothermophilus

Deposition date:

2006-04-25

Original release date:

2006-11-21

Authors:

Wienk, Hans; Tomaselli, Simona; Spurio, Roberto; Gualerzi, Claudio; Boelens, Rolf

Citation:

Citation: Milon, P.; Tischenko, E.; Tomsic, J.; Caserta, E.; Folkers, G.; La Teana, A.; Rodnina, M.; Pon, C.; Boelens, Rolf; Gualerzi, Claudio. "The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor" Proc. Natl. Acad. Sci. U.S.A. 103, 13962-13967 (2006).
PubMed: 16968770

Assembly members:

Assembly members:
domain III-IV, polymer, 240 residues, 26759 Da.

Natural source:

Natural source: Common Name: bacillus stearothermophilus Taxonomy ID: 1422 Superkingdom: Eubacteria Kingdom: not available Genus/species: Bacillus stearothermophilus

Experimental source:

Experimental source: Production method: recombinant technology Vector: pEV1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
domain III-IV: NEFELGTRGSSRVDLQEQRS VKTRVSLDDLFEQIKQGEMK ELNLIVKADVQGSVEALVAA LQKIDVEGVRVKIIHAAVGA ITESDISLATASNAIVIGFN VRPDANAKRAAESEKVDIRL HRIIYNVIEEIEAAMKGMLD EYEEKVIGQAEVRQTFKVSK VGTIAGCYVTDGKITRDSKV RLIRQGIVVYEGEIDSLKRY KDDVREVAQGYECGLTIKNF NDIKEGDVIEAYVMQEVARA

Data sets:

assigned_chemical_shifts
- chem_shift_list_1
heteronucl_NOEs
- heteronucl_NOE_list_1
heteronucl_T1_relaxation
- T1_list_1
heteronucl_T2_relaxation
- T2_list_1

Data type	Count
13C chemical shifts	332
15N chemical shifts	163
1H chemical shifts	163
heteronuclear NOE values	143
T1 relaxation values	145
T2 relaxation values	145

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	IF2 domain III-IV	1

Entities:

Entity 1, IF2 domain III-IV 240 residues - 26759 Da.

Please notice that since residue X is removed from Proline-deletion the numbering is dis-continuous.

1	ASN	GLU	PHE	GLU	LEU	GLY	THR	ARG	GLY	SER
2	SER	ARG	VAL	ASP	LEU	GLN	GLU	GLN	ARG	SER
3	VAL	LYS	THR	ARG	VAL	SER	LEU	ASP	ASP	LEU
4	PHE	GLU	GLN	ILE	LYS	GLN	GLY	GLU	MET	LYS
5	GLU	LEU	ASN	LEU	ILE	VAL	LYS	ALA	ASP	VAL
6	GLN	GLY	SER	VAL	GLU	ALA	LEU	VAL	ALA	ALA
7	LEU	GLN	LYS	ILE	ASP	VAL	GLU	GLY	VAL	ARG
8	VAL	LYS	ILE	ILE	HIS	ALA	ALA	VAL	GLY	ALA
9	ILE	THR	GLU	SER	ASP	ILE	SER	LEU	ALA	THR
10	ALA	SER	ASN	ALA	ILE	VAL	ILE	GLY	PHE	ASN
11	VAL	ARG	PRO	ASP	ALA	ASN	ALA	LYS	ARG	ALA
12	ALA	GLU	SER	GLU	LYS	VAL	ASP	ILE	ARG	LEU
13	HIS	ARG	ILE	ILE	TYR	ASN	VAL	ILE	GLU	GLU
14	ILE	GLU	ALA	ALA	MET	LYS	GLY	MET	LEU	ASP
15	GLU	TYR	GLU	GLU	LYS	VAL	ILE	GLY	GLN	ALA
16	GLU	VAL	ARG	GLN	THR	PHE	LYS	VAL	SER	LYS
17	VAL	GLY	THR	ILE	ALA	GLY	CYS	TYR	VAL	THR
18	ASP	GLY	LYS	ILE	THR	ARG	ASP	SER	LYS	VAL
19	ARG	LEU	ILE	ARG	GLN	GLY	ILE	VAL	VAL	TYR
20	GLU	GLY	GLU	ILE	ASP	SER	LEU	LYS	ARG	TYR
21	LYS	ASP	ASP	VAL	ARG	GLU	VAL	ALA	GLN	GLY
22	TYR	GLU	CYS	GLY	LEU	THR	ILE	LYS	ASN	PHE
23	ASN	ASP	ILE	LYS	GLU	GLY	ASP	VAL	ILE	GLU
24	ALA	TYR	VAL	MET	GLN	GLU	VAL	ALA	ARG	ALA

Samples:

sample_2: domain III-IV, [U-15N], 0.5 mM; potassium phosphate 20 mM; potassium chloride 200 mM; D2O, [U-2H], 10 % (v/v); EDTA-free protease inhibitor; sodium azide 0.02 % (w/v)

sample_1: domain III-IV, [U-13C; U-15N], 0.5 mM; Potassium phosphate 20 mM; potassium chloride 200 mM; D2O, [U-2H], 10 % (v/v); EDTA-free protease inhibitor; sodium azide 0.02 % (w/v)

conditions_1: pH: 5.2; temperature: 307 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H15N_HSQC	sample_2	not available	conditions_1
HNCA	sample_1	not available	conditions_1
HNCACB	sample_1	not available	conditions_1
CBCA(CO)NH	sample_1	not available	conditions_1
NOESY-[15N]-HSQC	sample_2	not available	conditions_1
R1-1H15N-HSQC	sample_2	not available	conditions_1
R2-1H15N-CPMG	sample_2	not available	conditions_1
1H15N-hetNOE	sample_2	not available	conditions_1

Software:

xwinnmr v3.5, BRUKER - acquisition of NMR spectra

NMRPipe, Frank Delaglio - processing of NMR spectra

NMRView v5.0.3, Bruce A. Johnson - spectral analysis and heteronuclear NOE calculation

CurveFit, A.G. Palmer III - fitting of signal intensities to obtain relaxation rates

NMR spectrometers:

Bruker Avance 600.13 MHz

BMRB	6577
PDB	1Z9B
DBJ	BAD75548 GAD12201 GAJ59418
EMBL	CAA27987
GB	ACX78663 ADI27260 ADU93636 AEV18768 AGE21726
REF	WP_011230763 WP_013145729 WP_013523417 WP_015374430 WP_020959388
SP	P04766 Q5L0I8
AlphaFold	P04766 Q5L0I8

1	ASN	GLU	PHE	GLU	LEU	GLY	THR	ARG	GLY	SER
2	SER	ARG	VAL	ASP	LEU	GLN	GLU	GLN	ARG	SER
3	VAL	LYS	THR	ARG	VAL	SER	LEU	ASP	ASP	LEU
4	PHE	GLU	GLN	ILE	LYS	GLN	GLY	GLU	MET	LYS
5	GLU	LEU	ASN	LEU	ILE	VAL	LYS	ALA	ASP	VAL
6	GLN	GLY	SER	VAL	GLU	ALA	LEU	VAL	ALA	ALA
7	LEU	GLN	LYS	ILE	ASP	VAL	GLU	GLY	VAL	ARG
8	VAL	LYS	ILE	ILE	HIS	ALA	ALA	VAL	GLY	ALA
9	ILE	THR	GLU	SER	ASP	ILE	SER	LEU	ALA	THR
10	ALA	SER	ASN	ALA	ILE	VAL	ILE	GLY	PHE	ASN
11	VAL	ARG	PRO	ASP	ALA	ASN	ALA	LYS	ARG	ALA
12	ALA	GLU	SER	GLU	LYS	VAL	ASP	ILE	ARG	LEU
13	HIS	ARG	ILE	ILE	TYR	ASN	VAL	ILE	GLU	GLU
14	ILE	GLU	ALA	ALA	MET	LYS	GLY	MET	LEU	ASP
15	GLU	TYR	GLU	GLU	LYS	VAL	ILE	GLY	GLN	ALA
16	GLU	VAL	ARG	GLN	THR	PHE	LYS	VAL	SER	LYS
17	VAL	GLY	THR	ILE	ALA	GLY	CYS	TYR	VAL	THR
18	ASP	GLY	LYS	ILE	THR	ARG	ASP	SER	LYS	VAL
19	ARG	LEU	ILE	ARG	GLN	GLY	ILE	VAL	VAL	TYR
20	GLU	GLY	GLU	ILE	ASP	SER	LEU	LYS	ARG	TYR
21	LYS	ASP	ASP	VAL	ARG	GLU	VAL	ALA	GLN	GLY
22	TYR	GLU	CYS	GLY	LEU	THR	ILE	LYS	ASN	PHE
23	ASN	ASP	ILE	LYS	GLU	GLY	ASP	VAL	ILE	GLU
24	ALA	TYR	VAL	MET	GLN	GLU	VAL	ALA	ARG	ALA

1	ASN	GLU	PHE	GLU	LEU	GLY	THR	ARG	GLY	SER
2	SER	ARG	VAL	ASP	LEU	GLN	GLU	GLN	ARG	SER
3	VAL	LYS	THR	ARG	VAL	SER	LEU	ASP	ASP	LEU
4	PHE	GLU	GLN	ILE	LYS	GLN	GLY	GLU	MET	LYS
5	GLU	LEU	ASN	LEU	ILE	VAL	LYS	ALA	ASP	VAL
6	GLN	GLY	SER	VAL	GLU	ALA	LEU	VAL	ALA	ALA
7	LEU	GLN	LYS	ILE	ASP	VAL	GLU	GLY	VAL	ARG
8	VAL	LYS	ILE	ILE	HIS	ALA	ALA	VAL	GLY	ALA
9	ILE	THR	GLU	SER	ASP	ILE	SER	LEU	ALA	THR
10	ALA	SER	ASN	ALA	ILE	VAL	ILE	GLY	PHE	ASN
11	VAL	ARG	PRO	ASP	ALA	ASN	ALA	LYS	ARG	ALA
12	ALA	GLU	SER	GLU	LYS	VAL	ASP	ILE	ARG	LEU
13	HIS	ARG	ILE	ILE	TYR	ASN	VAL	ILE	GLU	GLU
14	ILE	GLU	ALA	ALA	MET	LYS	GLY	MET	LEU	ASP
15	GLU	TYR	GLU	GLU	LYS	VAL	ILE	GLY	GLN	ALA
16	GLU	VAL	ARG	GLN	THR	PHE	LYS	VAL	SER	LYS
17	VAL	GLY	THR	ILE	ALA	GLY	CYS	TYR	VAL	THR
18	ASP	GLY	LYS	ILE	THR	ARG	ASP	SER	LYS	VAL
19	ARG	LEU	ILE	ARG	GLN	GLY	ILE	VAL	VAL	TYR
20	GLU	GLY	GLU	ILE	ASP	SER	LEU	LYS	ARG	TYR
21	LYS	ASP	ASP	VAL	ARG	GLU	VAL	ALA	GLN	GLY
22	TYR	GLU	CYS	GLY	LEU	THR	ILE	LYS	ASN	PHE
23	ASN	ASP	ILE	LYS	GLU	GLY	ASP	VAL	ILE	GLU
24	ALA	TYR	VAL	MET	GLN	GLU	VAL	ALA	ARG	ALA