BMRB Entry 53247

Name: A human ATG3 N-terminal deletion construct
Published: 2025-07-29

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR53247

NMR-STAR file interactive viewer.
NMR-STAR v3 text 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:

A human ATG3 N-terminal deletion construct

Deposition date:

2025-06-26

Original release date:

2025-07-29

Authors:

Ohashi, Kazuto; Otomo, Takanori

Citation:

Citation: Ohashi, Kazuto; Kroon, Gerard; Otomo, Takanori. "Structural Insights into the GABARAP-ATG3 Backside Interaction and Apo ATG3 Conformation" Biochemistry 64, 3178-3189 (2025).
PubMed: 40628661

Assembly members:

Assembly members:
entity_1, polymer, 290 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: pGEX

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSKFKETGVITPEEFVAAGD HLVHHCPTWQWATGEELKVK AYLPTGKQFLVTKNVPCYKR CKQMEYSDELEAIIEEDDGD GGWVDTYHNTGITGITEAVK EITLENKDNIRLQDCSALCE EEEDEDEGEAADMEEYEESG LLETDEATLDTRKIVEACKA KTDAGGEDAILQTRTYDLYI TYDKYYQTPRLWLFGYDEQR QPLTVEHMYEDISQDHVKKT VTIENHPHLPPPPMCSVHPC RHAEVMKKIIETVAEGGGEL GVHMYLLIFLKFVQAVIPTI EYDYTRHFTM

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	309
15N chemical shifts	103
1H chemical shifts	103

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ATG3 delta N	1

Entities:

Entity 1, ATG3 delta N 290 residues - Formula weight is not available

G+(ATG3 residues 26-314)

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

Samples:

sample_1: ATG3 delta N double-labeled, [U-100% 13C; U-100% 15N], 0.6 mM

sample_conditions_1: ionic strength: 150 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1

Software:

NMRDraw - processing

NMRPipe - processing

NMRViewJ - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III 800 MHz

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

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