BMRB Entry 50831

Name: 1H, 15N, 13C, backbone resonance assignment of the 5'-GG(m6A)CT-3' bound human Alkbh5, pH 6.0
Published: 2021-04-06

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50831

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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:

1H, 15N, 13C, backbone resonance assignment of the 5'-GG(m6A)CT-3' bound human Alkbh5, pH 6.0

Deposition date:

2021-03-14

Original release date:

2021-04-06

Authors:

Purslow, Jeffrey; Venditti, Vincenzo

Citation:

Citation: Purslow, Jeffrey; Nguyen, Trang; Khatiwada, Balabhadra; Singh, Aayushi; Venditti, Vincenzo. "N 6-methyladenosine binding induces a metal-centered rearrangement that activates the human RNA demethylase Alkbh5" Sci. Adv. 7, eabi8215-eabi8215 (2021).
PubMed: 34407931

Assembly members:

Assembly members:
entity_1, polymer, 230 residues, Formula weight is not available
entity_ZN, non-polymer, 65.409 Da.
entity_AKG, non-polymer, 146.098 Da.
entity_4, polymer, 5 residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: Modified pET21a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SHMPERSDYEEQQLQKEEEA RKVKSGIRQMRLFSQDECAK IEARIDEVVSRAEKGLYNEH TVDRAPLRNKYFFGEGYTYG AQLQKRGPGQERLYPPGDVD EIPEWVHQLVIQKLVEHRVI PEGFVNSAVINDYQPGGCIV SHVDPIHIFERPIVSVSFFS DSALCFGCKFQFKPIRVSEP VLSLPVRRGSVTVLSGYAAD EITHCIRPQDIKERRAVIIL RKTRLDAPRL
entity_4: GGXCT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	1115
15N chemical shifts	344
1H chemical shifts	344

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Alkbh5 66-292, chain 1	1
2	Alkbh5 66-292, chain 2	1
3	ZN ion	2
4	AKG	3
5	GG(m6A)CT	4

Entities:

Entity 1, Alkbh5 66-292, chain 1 230 residues - Formula weight is not available

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

Entity 2, ZN ion - Zn - 65.409 Da.

1

ZN

Entity 3, AKG - C5 H6 O5 - 146.098 Da.

1

AKG

Entity 4, GG(m6A)CT 5 residues - Formula weight is not available

1

DG

6MZ

DC

DT

Samples:

sample_1: Alkbh5 Residues 66-292, [U-13C; U-15N; U-2H], 0.45 mM; MES 20 mM; NaCl 150 mM; ZnCl2 0.1 mM; a-KG 1 mM

sample_conditions_1: ionic strength: 150 mM; pH: 6.0; pressure: 1 atm; temperature: 273 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 HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1

Software:

SPARKY - chemical shift assignment

NMR spectrometers:

Bruker Avance II 600 MHz

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

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

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

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