BMRB Entry 18135

Name: A single GalNAc residue on Threonine-106 modifies the dynamics and the structure of Interferon alpha-2a around the glycosylation site.
Published: 2012-12-04

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PDB ID: 2lms
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18135
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

A single GalNAc residue on Threonine-106 modifies the dynamics and the structure of Interferon alpha-2a around the glycosylation site.

Deposition date:

2011-12-12

Original release date:

2012-12-04

Authors:

Ghasriani, Houman; Belcourt, Pascal; Sauve, Simon; Hodgson, Derek; Gingras, Genevieve; Brochu, Denis; Gilbert, Michel; Aubin, Yves

Citation:

Citation: Ghasriani, Houman; Belcourt, Pascal; Sauve, Simon; Hodgson, Derek; Brochu, Denis; Gilbert, Michel; Aubin, Yves. "A single N-acetylgalactosamine residue at threonine 106 modifies the dynamics and structure of interferon 2a around the glycosylation site." J. Biol. Chem. 288, 247-254 (2013).
PubMed: 23184955

Assembly members:

Assembly members:
Interferon_Alpha-2a, polymer, 165 residues, 19264.242 Da.
A2G, non-polymer, 221.208 Da.

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: pET-15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Interferon_Alpha-2a: CDLPQTHSLGSRRTLMLLAQ MRKISLFSCLKDRHDFGFPQ EEFGNQFQKAETIPVLHEMI QQIFNLFSTKDSSAAWDETL LDKFYTELYQQLNDLEACVI QGVGVTETPLMKEDSILAVR KYFQRITLYLKEKKYSPCAW EVVRAEIMRSFSLSTNLQES LRSKE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	731
15N chemical shifts	178
1H chemical shifts	1197

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	SUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE)	2

Entities:

Entity 1, entity_1 165 residues - 19264.242 Da.

O-glycosylation at Thr106, with N-Acetyl-D-Galactosamine(alpha).

1

CYS

ASP

LEU

PRO

GLN

THR

HIS

SER

LEU

GLY

2

SER

ARG

THR

LEU

MET

LEU

ALA

GLN

3

MET

ARG

LYS

ILE

SER

LEU

PHE

SER

CYS

LEU

4

LYS

ASP

ARG

HIS

ASP

PHE

GLY

PHE

PRO

GLN

5

GLU

PHE

GLY

ASN

GLN

PHE

GLN

LYS

ALA

6

GLU

THR

ILE

PRO

VAL

LEU

HIS

GLU

MET

ILE

7

GLN

ILE

PHE

ASN

LEU

PHE

SER

THR

LYS

8

ASP

SER

ALA

TRP

ASP

GLU

THR

LEU

9

LEU

ASP

LYS

PHE

TYR

THR

GLU

LEU

TYR

GLN

10

GLN

LEU

ASN

ASP

LEU

GLU

ALA

CYS

VAL

ILE

11

GLN

GLY

VAL

GLY

VAL

THR

GLU

THR

PRO

LEU

12

MET

LYS

GLU

ASP

SER

ILE

LEU

ALA

VAL

ARG

13

LYS

TYR

PHE

GLN

ARG

ILE

THR

LEU

TYR

LEU

14

LYS

GLU

LYS

TYR

SER

PRO

CYS

ALA

TRP

15

GLU

VAL

ARG

ALA

GLU

ILE

MET

ARG

SER

16

PHE

SER

LEU

SER

THR

ASN

LEU

GLN

GLU

SER

17

LEU

ARG

SER

LYS

GLU

Entity 2, SUGAR (N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE) - C8 H15 N O6 - 221.208 Da.

1

A2G

Samples:

sample_1: Interferon Alpha-2a (O-glycosylated), [U-100% 13C; U-100% 15N], 0.85 mM; Denaturated Sodium Acetate 25 mM; H2O 90%; D2O 10%

sample_2: Interferon Alpha-2a (O-glycosylated), [U-100% 13C; U-100% 15N], 0.53 mM; Deuturated Sodium Acetate 25 mM; H2O 90%; D2O 10%

sample_3: Interferon Alpha-2a (O-glycosylated), [U-100% 13C; U-100% 15N], 0.87 mM; Deuturated Sodium Acetate 25 mM; D2O 100%

sample_conditions_1: ionic strength: 25 mM; pH: 3.5; pressure: 1 atm; temperature: 298.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
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 HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
2D (hb)CB(cgcd)HD	sample_3	isotropic	sample_conditions_1
2D (hb)CB(cgcdce)HE	sample_3	isotropic	sample_conditions_1
4D (C13)HSQC-NOESY-(N15)HSQC	sample_1	isotropic	sample_conditions_1
4D (C13)HSQC-NOESY-(C13)HSQC	sample_3	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Bruker Avance 700 MHz
Bruker Avance III 600 MHz

BMRB	16677 18344 4081
PDB	1ITF 1RH2 2HYM 2KZ1 2LAG 2LMS 3S9D 3SE3 4YPG 4Z5R
DBJ	BAJ20902
EMBL	CAA23805 CAA23809 CAA23810 CAA25770 CAA46954
GB	AAA52715 AAA59181 AAB59402 AAC64915 AAH74936
PRF	0611561A 0906342A
REF	NP_000596 XP_003830724 XP_004047919 XP_528568
SP	P01563
AlphaFold	P01563