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Found 1 Document (0.861 seconds)

BMRB: 18135

2LMS

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

Authors

Ghasriani, H., Belcourt, P., Sauve, S., Hodgson, D.J., Gingras, G., Brochu, D., Gilbert, M., Aubin, Y.

Assembly

GLYCOSYLATED HUMAN INTERFERON ALPHA-2A [WITH GALNAC AT THR 106]

Entity

1. Interferon Alpha-2a (polymer, Thiol state: all disulfide bound), 165 monomers, 19240.89 Da Detail

CDLPQTHSLG SRRTLMLLAQ MRKISLFSCL KDRHDFGFPQ EEFGNQFQKA ETIPVLHEMI QQIFNLFSTK DSSAAWDETL LDKFYTELYQ QLNDLEACVI QGVGVTETPL MKEDSILAVR KYFQRITLYL KEKKYSPCAW EVVRAEIMRS FSLSTNLQES LRSKE

2. A2G (non-polymer), 221.208 Da

Total weight

19462.098 Da

Max. entity weight

19240.89 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS1:SG	1:CYS98:SG
2	disulfide	sing	1:CYS29:SG	1:CYS138:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.7 %, Completeness (bb): 99.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.7 % (1929 of 2016)	96.4 % (1016 of 1054)	93.8 % (735 of 784)	100.0 % (178 of 178)
Backbone	99.4 % (974 of 980)	100.0 % (330 of 330)	98.8 % (484 of 490)	100.0 % (160 of 160)
Sidechain	93.2 % (1115 of 1196)	94.8 % (686 of 724)	90.5 % (411 of 454)	100.0 % (18 of 18)
Aromatic	77.8 % (137 of 176)	88.6 % (78 of 88)	66.3 % (57 of 86)	100.0 % (2 of 2)
Methyl	100.0 % (180 of 180)	100.0 % (90 of 90)	100.0 % (90 of 90)

1. Interferon Alpha-2a

CDLPQTHSLG SRRTLMLLAQ MRKISLFSCL KDRHDFGFPQ EEFGNQFQKA ETIPVLHEMI QQIFNLFSTK DSSAAWDETL LDKFYTELYQ QLNDLEACVI QGVGVTETPL MKEDSILAVR KYFQRITLYL KEKKYSPCAW EVVRAEIMRS FSLSTNLQES LRSKE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
1	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.85 mM
2	Denaturated Sodium Acetate	natural abundance	25 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
5	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.53 mM
6	Deuturated Sodium Acetate	natural abundance	25 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
9	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.87 mM
10	Deuturated Sodium Acetate	natural abundance	25 mM
11	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LMS, Strand ID: A Detail

Release date

2012-12-03

Citation

A single N-acetylgalactosamine residue at threonine 106 modifies the dynamics and structure of interferon α2a around the glycosylation site
Ghasriani, H., Belcourt, P.J.F., Sauve, S., Hodgson, D.J., Brochu, D., Gilbert, M., Aubin, Y.
J. Biol. Chem. (2013), 288, 247-254, PubMed 23184955 , DOI 10.1074/jbc.M112.413252 , Abstract

Related entities 1. Interferon Alpha-2a, : 1 : 7 : 1 : 138 entities Detail

Interaction partners 1. Interferon Alpha-2a, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 14 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
1	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.85 mM
2	Denaturated Sodium Acetate	natural abundance	25 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

2 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
1	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.85 mM
2	Denaturated Sodium Acetate	natural abundance	25 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

3 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
1	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.85 mM
2	Denaturated Sodium Acetate	natural abundance	25 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
1	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.85 mM
2	Denaturated Sodium Acetate	natural abundance	25 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

5 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
1	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.85 mM
2	Denaturated Sodium Acetate	natural abundance	25 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
1	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.85 mM
2	Denaturated Sodium Acetate	natural abundance	25 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
1	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.85 mM
2	Denaturated Sodium Acetate	natural abundance	25 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
9	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.87 mM
10	Deuturated Sodium Acetate	natural abundance	25 mM
11	D2O	natural abundance	100 %

9 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
9	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.87 mM
10	Deuturated Sodium Acetate	natural abundance	25 mM
11	D2O	natural abundance	100 %

10 3D C(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
1	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.85 mM
2	Denaturated Sodium Acetate	natural abundance	25 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

11 2D (hb)CB(cgcd)HD

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
9	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.87 mM
10	Deuturated Sodium Acetate	natural abundance	25 mM
11	D2O	natural abundance	100 %

12 2D (hb)CB(cgcdce)HE

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
9	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.87 mM
10	Deuturated Sodium Acetate	natural abundance	25 mM
11	D2O	natural abundance	100 %

13 4D (C13)HSQC-NOESY-(N15)HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
1	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.85 mM
2	Denaturated Sodium Acetate	natural abundance	25 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

14 4D (C13)HSQC-NOESY-(C13)HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298.15 K, pH 3.5, Details Buffer: 25mM Deuturated Sodium Acetate at pH 3.5.

#	Name	Isotope labeling	Concentration
9	Interferon Alpha-2a (O-glycosylated)	[U-100% 13C; U-100% 15N]	0.87 mM
10	Deuturated Sodium Acetate	natural abundance	25 mM
11	D2O	natural abundance	100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18135_2lms.nef
Input source #2: Coordindates	2lms.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:1:CYS:SG	A:98:CYS:SG	oxidized, CA 55.949, CB 41.684 ppm	oxidized, CA 57.166, CB 41.879 ppm	2.141
A:29:CYS:SG	A:138:CYS:SG	oxidized, CA 53.43, CB 37.242 ppm	oxidized, CA 57.095, CB 36.779 ppm	1.946

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:107:THR:OG1	2:1:A2G:C1	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	Assigned chemical shifts

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
MCDLPQTHSLGSRRTLMLLAQMRKISLFSCLKDRHDFGFPQEEFGNQFQKAETIPVLHEMIQQIFNLFSTKDSSAAWDETLLDKFYTELYQQLNDLEACV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MCDLPQTHSLGSRRTLMLLAQMRKISLFSCLKDRHDFGFPQEEFGNQFQKAETIPVLHEMIQQIFNLFSTKDSSAAWDETLLDKFYTELYQQLNDLEACV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------110-------120-------130-------140-------150-------160-----
IQGVGVTETPLMKEDSILAVRKYFQRITLYLKEKKYSPCAWEVVRAEIMRSFSLSTNLQESLRSKE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IQGVGVTETPLMKEDSILAVRKYFQRITLYLKEKKYSPCAWEVVRAEIMRSFSLSTNLQESLRSKE
-------110-------120-------130-------140-------150-------160------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	166	0	0	100.0

Content subtype: combined_18135_2lms.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1916		99.4 (chain: A, length: 166), 100.0 (chain: B, length: 1)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3599 (1)	noe	98.8 (chain: A, length: 166)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	257 (257)	.	88.0 (chain: A, length: 166)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 166, Sequence coverage: 99.4%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 1007
  - ¹³C chemical shifts: 731
  - ¹⁵N chemical shifts: 178
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1061	1003	94.5
¹³C chemical shifts	789	730	92.5
¹⁵N chemical shifts	188	178	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	332	330	99.4
¹³C chemical shifts	332	324	97.6
¹⁵N chemical shifts	161	160	99.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	729	673	92.3
¹³C chemical shifts	457	406	88.8
¹⁵N chemical shifts	27	18	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	96	95	99.0
¹³C chemical shifts	96	95	99.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	88	78	88.6
¹³C chemical shifts	86	57	66.3
¹⁵N chemical shifts	2	2	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	2	22.2
¹³C chemical shifts	8	1	12.5
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	7	1	14.3
¹³C chemical shifts	6	1	16.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	1	50.0
¹³C chemical shifts	2	0	0.0
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1	1	100.0
¹³C chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 166, Sequence coverage: 98.8%
- Total number of restraints: 3599
- Weight of restraints: 1.0 (3599)
- Potential type of restraints: upper-bound-parabolic (3599)
- Range of distance target values: 1.8, 6.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 166, Sequence coverage: 88.0%
- Total number of restraints: 257
- Total number of restraints per polymer type: 257
- Weight of restraints: 1.0 (257)
- Potential type of restraints: square-well-parabolic (257)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords CYTOKINE, DYNAMICS, GLYCOPROTEIN, INTERFERON, NMR, O-GLYCOSYLATION, SIGNALING PROTEIN, STRUCTURE, TYPE I INTERFERONS

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Found 1 Document (0.861 seconds)

BMRB: 18135

Sample #1

Sample #2

Sample #3

Related entities 1. Interferon Alpha-2a, : 1 : 7 : 1 : 138 entities Detail

Interaction partners 1. Interferon Alpha-2a, : 1 interactors Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 4 contents Detail