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- PDB-3chn: Solution structure of human secretory IgA1 -

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Basic information

Entry
Database: PDB / ID: 3chn
TitleSolution structure of human secretory IgA1
Components
  • (Secretory component) x 2
  • Ig alpha-1 chain C region
  • Immunoglobulin kappa light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin A / Secretory immunoglobulin A / Mucosal immunity / neutron scattering / X-ray scattering / Chromophore / Glycoprotein / Immunoglobulin C region / Immunoglobulin domain / Membrane / Phosphoprotein / Secreted / Transmembrane
Function / homology
Function and homology information


polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / Fc receptor signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / glomerular filtration / IgA immunoglobulin complex ...polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / Fc receptor signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / glomerular filtration / IgA immunoglobulin complex / azurophil granule membrane / receptor clustering / immunoglobulin complex, circulating / IgG immunoglobulin complex / positive regulation of respiratory burst / Scavenging of heme from plasma / complement activation, classical pathway / antigen binding / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / epidermal growth factor receptor signaling pathway / antibacterial humoral response / blood microparticle / adaptive immune response / receptor complex / immune response / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...Immunoglobulin / Immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Polymeric immunoglobulin receptor / Immunoglobulin heavy constant alpha 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING / SYNCHROTRON / CONSTRAINED MODELLING
AuthorsBonner, A. / Almogren, A. / Furtado, P.B. / Kerr, M.A. / Perkins, S.J.
Citation
Journal: Mucosal Immunol / Year: 2009
Title: Location of secretory component on the Fc edge of dimeric IgA1 reveals insight into the role of secretory IgA1 in mucosal immunity.
Authors: Bonner, A. / Almogren, A. / Furtado, P.B. / Kerr, M.A. / Perkins, S.J.
#1: Journal: J. Immunol. / Year: 2008
Title: Implications of the near-planar solution structure of human myeloma dimeric IgA1 for mucosal immunity and IgA nephropathy
Authors: Bonner, A. / Furtado, P.B. / Almogren, A. / Kerr, M.A. / Perkins, S.J.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: The Fab and Fc fragments of IgA1 exhibit a different arrangement from that in IgG: a study by X-ray and neutron solution scattering and homology modelling
Authors: Boehm, M.K. / Woof, J.M. / Kerr, M.A. / Perkins, S.J.
#3: Journal: J.Biol.Chem. / Year: 2007
Title: Solution structure of human secretory component and implication for biological function
Authors: Bonner, A. / Perrier, C. / Corthesy, B. / Perkins, S.J.
History
DepositionMar 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Other
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Jun 13, 2018Group: Data collection / Database references / Category: citation / diffrn_radiation / diffrn_source
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _diffrn_radiation.diffrn_id / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_scattering_type / _diffrn_source.source
Revision 1.5Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source / _diffrn_source.type
Revision 1.6Dec 18, 2019Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.7Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Immunoglobulin kappa light chain
M: Immunoglobulin kappa light chain
N: Immunoglobulin kappa light chain
O: Immunoglobulin kappa light chain
A: Ig alpha-1 chain C region
B: Ig alpha-1 chain C region
D: Ig alpha-1 chain C region
C: Ig alpha-1 chain C region
J: Secretory component
S: Secretory component


Theoretical massNumber of molelcules
Total (without water)373,34610
Polymers373,34610
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Number of models10
DetailsThe biological assembly of SIgA1 consists of four IgA1 heavy chains (A,B,C and D), four light chains (L, M, N and O), J chain (J) and secretory component (S).

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Components

#1: Antibody
Immunoglobulin kappa light chain / Coordinate model: Cα atoms only


Mass: 23216.770 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: purified from human colostrum / Source: (natural) Homo sapiens (human)
#2: Antibody
Ig alpha-1 chain C region / Coordinate model: Cα atoms only


Mass: 51068.383 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: purified from human colostrum / Source: (natural) Homo sapiens (human) / References: UniProt: P01876
#3: Protein Secretory component / / Poly-Ig receptor / PIGR / Hepatocellular carcinoma-associated protein TB6 / Coordinate model: Cα atoms only


Mass: 11850.517 Da / Num. of mol.: 1 / Fragment: Ig-like V-type domain 4 / Source method: isolated from a natural source / Details: purified from human colostrum / Source: (natural) Homo sapiens (human) / References: UniProt: P01833
#4: Protein Secretory component / / Poly-Ig receptor / PIGR / Hepatocellular carcinoma-associated protein TB6 / Coordinate model: Cα atoms only


Mass: 64355.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purified from human colostrum / Source: (natural) Homo sapiens (human) / References: UniProt: P01833
Sequence detailsTHE PART OF SEQUENCE BELONGS TO IGA VARIABLE HEAVY CHAIN.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12881
22881
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID211
SPALLATION SOURCEISISLOQ22.0-10.0
Detector
TypeIDDetectorDate
FRELON1CCDNov 1, 2001
3-He ORDELA2AREA DETECTORJul 1, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2TIME OF FLIGHTLAUELneutron1
1MIRRORSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
221
3101
Soln scatter

Buffer name: 140 MM NACL 12.5 MM NAHPO4 0.5 MM EDTA 0.02% NA AZIDE / Data analysis software list: SCTPL7, GNOM / Protein length: 1 / Sample pH: 7.5 / Source class: Y / Temperature: 288 K

TypeIDConc. range (mg/ml)Data reduction software listDetector typeMax mean cross sectional radii gyration (nm)Max mean cross sectional radii gyration esd (nm)Mean guiner radius (nm)Mean guiner radius esd (nm)Min mean cross sectional radii gyration (nm)Min mean cross sectional radii gyration esd (nm)Num. of time framesSource beamlineSource type
x-ray10.30-0.60MULTICCDFRELON CCD CAMERA1.30.068.290.23.950.1310ID2ESRF GRENOBLE
neutron20.6COLETTEHE-3 ORDELA DETECTOR7.221LOQISIS RUTHERFORD- APPLETON LAB

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Processing

Software
NameVersionClassification
SCTPL7model building
GNOMmodel building
Insight IIII 98model building
COLETTE(ISIS) ID2 (ESRF)data scaling
SCTPL7phasing
GNOMphasing
RefinementMethod to determine structure: CONSTRAINED MODELLING
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 0 0 3447
Soln scatter modelDetails: THE COORDINATES CONTAIN ONLY CA ATOMS. THE TEN BEST-FIT SOLUTION STRUCTURES HAVE BEEN DEPOSITED, WHERE MODEL 1 IS THE BEST-FIT SIGA1 SOLUTION STRUCTURE AND MODELS 2 TO 10 REPRESENT THE REST ...Details: THE COORDINATES CONTAIN ONLY CA ATOMS. THE TEN BEST-FIT SOLUTION STRUCTURES HAVE BEEN DEPOSITED, WHERE MODEL 1 IS THE BEST-FIT SIGA1 SOLUTION STRUCTURE AND MODELS 2 TO 10 REPRESENT THE REST OF THE FAMILY OF BEST-FIT STRUCTURES.
Num. of conformers submitted: 10 / Representative conformer: 1 / Software list: INSIGHT II, SCTPL7, GNOM

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