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- PDB-2lms: A single GalNAc residue on Threonine-106 modifies the dynamics an... -

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Basic information

Entry
Database: PDB / ID: 2lms
TitleA single GalNAc residue on Threonine-106 modifies the dynamics and the structure of Interferon alpha-2a around the glycosylation site
ComponentsInterferon alpha-2
KeywordsIMMUNE SYSTEM / CYTOKINE / GLYCOPROTEIN / O-GLYCOSYLATION / SIGNALING PROTEIN / TYPE I INTERFERONS
Function / homology
Function and homology information


type I interferon receptor binding / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / negative regulation of viral entry into host cell ...type I interferon receptor binding / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / negative regulation of viral entry into host cell / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / response to exogenous dsRNA / B cell proliferation / humoral immune response / Regulation of IFNA/IFNB signaling / B cell differentiation / cytokine activity / Evasion by RSV of host interferon responses / cellular response to virus / cytokine-mediated signaling pathway / Interferon alpha/beta signaling / cell-cell signaling / Factors involved in megakaryocyte development and platelet production / collagen-containing extracellular matrix / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region
Similarity search - Function
Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / Interferon alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsGhasriani, H. / Belcourt, P.J.F. / Sauve, S. / Hodgson, D.J. / Gingras, G. / Brochu, D. / Gilbert, M. / Aubin, Y.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: A single N-acetylgalactosamine residue at threonine 106 modifies the dynamics and structure of interferon alpha2a around the glycosylation site.
Authors: Ghasriani, H. / Belcourt, P.J. / Sauve, S. / Hodgson, D.J. / Brochu, D. / Gilbert, M. / Aubin, Y.
History
DepositionDec 12, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jun 14, 2023Group: Database references / Other / Structure summary / Category: chem_comp / database_2 / pdbx_database_status
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6162
Polymers19,3951
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Interferon alpha-2 / IFN-alpha-2 / Interferon alpha-A / LeIF A


Mass: 19395.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P01563
#2: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HBHA(CO)NH
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1823D 1H-13C NOESY aliphatic
1923D 1H-13C NOESY aromatic
11013D C(CO)NH
11122D (hb)CB(cgcd)HD
11222D (hb)CB(cgcdce)HE
11314D (C13)HSQC-NOESY-(N15)HSQC
11424D (C13)HSQC-NOESY-(C13)HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.85 mM [U-100% 13C; U-100% 15N] Interferon Alpha-2a (O-glycosylated), 90% H2O/10% D2O90% H2O/10% D2O
20.87 mM [U-100% 13C; U-100% 15N] Interferon Alpha-2a (O-glycosylated), 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.85 mMInterferon Alpha-2a (O-glycosylated)-1[U-100% 13C; U-100% 15N]1
0.53 mMInterferon Alpha-2a (O-glycosylated)-2[U-100% 13C; U-100% 15N]2
0.87 mMInterferon Alpha-2a (O-glycosylated)-3[U-100% 13C; U-100% 15N]3
Sample conditionsIonic strength: 25 / pH: 3.5 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker Avance IIIBrukerAVANCE III6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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