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- PDB-2qtj: Solution structure of human dimeric immunoglobulin A -

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Basic information

Entry
Database: PDB / ID: 2qtj
TitleSolution structure of human dimeric immunoglobulin A
Components
  • Ig alpha-1 chain C region
  • Kappa light chain IgA1
KeywordsIMMUNE SYSTEM / X-ray and neutron solution scattering / immunology / antibody / immunoglobulin A1 / Chromophore / Glycoprotein / Immunoglobulin C region / Immunoglobulin domain
Function / homology
Function and homology information


secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / IgA immunoglobulin complex / IgG immunoglobulin complex / positive regulation of respiratory burst / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding ...secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / IgA immunoglobulin complex / IgG immunoglobulin complex / positive regulation of respiratory burst / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / Cell surface interactions at the vascular wall / antigen binding / B cell receptor signaling pathway / antibacterial humoral response / adaptive immune response / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...Immunoglobulin / Immunoglobulin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
Immunoglobulin heavy constant alpha 1 / Uncharacterized protein DKFZp686J11235
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING
AuthorsBonner, A. / Furtado, P.B. / Almogren, A. / Kerr, M.A. / Perkins, S.J.
CitationJournal: 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.
History
DepositionAug 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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

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Assembly

Deposited unit
L: Kappa light chain IgA1
M: Kappa light chain IgA1
A: Ig alpha-1 chain C region
B: Ig alpha-1 chain C region
N: Kappa light chain IgA1
O: Kappa light chain IgA1
C: Ig alpha-1 chain C region
D: Ig alpha-1 chain C region


Theoretical massNumber of molelcules
Total (without water)297,1418
Polymers297,1418
Non-polymers00
Water00
1
L: Kappa light chain IgA1
M: Kappa light chain IgA1
A: Ig alpha-1 chain C region
B: Ig alpha-1 chain C region


Theoretical massNumber of molelcules
Total (without water)148,5704
Polymers148,5704
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: Kappa light chain IgA1
O: Kappa light chain IgA1
C: Ig alpha-1 chain C region
D: Ig alpha-1 chain C region


Theoretical massNumber of molelcules
Total (without water)148,5704
Polymers148,5704
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Number of models10
DetailsTwo light chains (L and M or N and O) bind to two heavy chains (A and B or C and D) within each IgA monomer. Two IgA monomers then form the dimeric IgA molecule.

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Components

#1: Antibody
Kappa light chain IgA1 / Coordinate model: Cα atoms only


Mass: 23216.770 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Dimeric IgA1 was purified by thiophilic and jacalin affinity chromatography.
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: Kappa light chain dimeric IgA1 was isolated from myeloma serum.
Source: (natural) Homo sapiens (human) / References: UniProt: P01876, UniProt: Q6MZW0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Data collection

DetectorDate: Jul 1, 2001
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
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-ray10.58-1.16MULTICCDFRELON CCD CAMERA1.430.078.650.273.940.1810IDO2ESRF GRENOBLE
neutron20.83-1.16COLETTEHE-3 ORDELA DETECTOR7.60.051LOQISIS RUTHERFORD-APPLETON LAB

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Processing

Software
NameVersionClassification
SCTPL7model building
GNOMmodel building
Insight IIII 98model building
COLETTE(ISIS)data scaling
SCTPL7phasing
GNOMphasing
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 0 0 2756
Soln scatter modelNum. of conformers submitted: 10 / Representative conformer: 1 / Software list: INSIGHT II, SCTPL7, GNOM

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