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- PDB-3cm9: Solution Structure of Human SIgA2 -

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Basic information

Entry
Database: PDB / ID: 3cm9
TitleSolution Structure of Human SIgA2
Components
  • (Secretory component) x 2
  • Immunoglobulin heavy chain
  • Immunoglobulin light chain
KeywordsIMMUNE SYSTEM / Secretory IgA2 / Secretory IgA1 / IgA / mucosal immunity / X-ray and neutron scattering / constrained modelling / 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 IgA immunoglobulin complex / Fc receptor signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / azurophil granule membrane / receptor clustering / epidermal growth factor receptor signaling pathway / receptor complex ...polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / secretory IgA immunoglobulin complex / Fc receptor signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / azurophil granule membrane / receptor clustering / epidermal growth factor receptor signaling pathway / receptor complex / Neutrophil degranulation / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Polymeric immunoglobulin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING / SYNCHROTRON / CONSTRAINED SCATTERING MODELLING
AuthorsBonner, A. / Almogren, A. / Furtado, P.B. / Kerr, M.A. / Perkins, S.J.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: The nonplanar secretory IgA2 and near planar secretory IgA1 solution structures rationalize their different mucosal immune responses.
Authors: Bonner, A. / Almogren, A. / Furtado, P.B. / Kerr, M.A. / Perkins, S.J.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Solution structure determination of monomeric human IgA2 by X-ray and neutron scattering, analytical ultracentrifugation and constrained mdoelling: a comparison with monomeric human IgA1
Authors: Furtado, P.B. / Whitty, P.W. / Robertson, A. / Eaton, J.T. / Almogren, A. / Kerr, M.A. / Woof, J.M. / Perkins, S.J.
#2: Journal: To be Published
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.
History
DepositionMar 21, 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 / Category: diffrn_radiation / diffrn_source
Item: _diffrn_radiation.diffrn_id / _diffrn_radiation.pdbx_diffrn_protocol ..._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 1.7Apr 8, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / pdbx_entry_details / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_nat.common_name ..._entity.pdbx_description / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_entry_details.sequence_details / _struct.pdbx_descriptor / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.8Feb 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
Remark 265 EXPERIMENTAL DETAILS EXPERIMENT TYPE : X-RAY SOLUTION SCATTERING DATA ACQUISITION ... EXPERIMENTAL DETAILS EXPERIMENT TYPE : X-RAY SOLUTION SCATTERING DATA ACQUISITION RADIATION/NEUTRON SOURCE :ESRF GRENOBLE SYNCHROTRON (Y/N) :Y BEAMLINE :ID2 BEAMLINE INSTRUMENT :NULL DETECTOR TYPE :FRELON CCD CAMERA DETECTOR MANUFACTURER DETAILS :NULL TEMPERATURE (KELVIN) :288 PH :7.5 NUMBER OF TIME FRAMES USED :10 PROTEIN CONCENTRATION RANGE (MG/ML) :0.32-0.90 SAMPLE BUFFER :140 MM NACL :12.5 MM NAHPO4 :0.5 MM EDTA :0.02% NA AZIDE DATA REDUCTION SOFTWARE :MULTICCD DATA ANALYSIS SOFTWARE :SCTPL7, GNOM GUINIER MEAN RADIUS OF GYRATION (NM) :8.13 SIGMA MEAN RADIUS OF GYRATION :0.10 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) :4.22 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII :0.09 R(XS-2) MEAN CROSS SECTIONAL RADII (NM) :1.93 R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII :0.03 P(R) PROTEIN LENGTH (NM) :26 P(R) SIGMA PROTEIN LENGTH :1 EXPERIMENTAL DETAILS EXPERIMENT TYPE : NEUTRON SOLUTION SCATTERING DATA ACQUISITION RADIATION/NEUTRON SOURCE :ISIS RUTHERFORD- :APPLETON LAB SYNCHROTRON (Y/N) :Y BEAMLINE :LOQ BEAMLINE INSTRUMENT :NULL DETECTOR TYPE :HE-3 ORDELA :DETECTOR DETECTOR MANUFACTURER DETAILS :NULL TEMPERATURE (KELVIN) :288 PH :7.5 NUMBER OF TIME FRAMES USED :1 PROTEIN CONCENTRATION RANGE (MG/ML) :1.94 SAMPLE BUFFER :140 MM NACL :12.5 MM NAHPO4 :0.5 MM EDTA :0.02% NA AZIDE DATA REDUCTION SOFTWARE :COLETTE DATA ANALYSIS SOFTWARE :SCTPL7, GNOM GUINIER MEAN RADIUS OF GYRATION (NM) :7.57 SIGMA MEAN RADIUS OF GYRATION :NULL R(XS-1) MEAN CROSS SECTIONAL RADII (NM) :NULL R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII :NULL R(XS-2) MEAN CROSS SECTIONAL RADII (NM) :NULL R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII :NULL P(R) PROTEIN LENGTH (NM) :24 P(R) SIGMA PROTEIN LENGTH :1

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin heavy chain
B: Immunoglobulin heavy chain
C: Immunoglobulin heavy chain
D: Immunoglobulin heavy chain
J: Secretory component
L: Immunoglobulin light chain
M: Immunoglobulin light chain
N: Immunoglobulin light chain
O: Immunoglobulin light chain
S: Secretory component


Theoretical massNumber of molelcules
Total (without water)368,76110
Polymers368,76110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Number of models10
DetailsSecretory IgA2 is composed of four heavy chains (A, B, C, D) and four light chains (L, M, N, O), J chain (J) and secretory component (S)

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Components

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


Mass: 49922.031 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: purified from human colostrum / Source: (natural) Homo sapiens (human)
#2: Protein Secretory component / 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
#3: Antibody
Immunoglobulin 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)
#4: Protein Secretory component / 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 A,B,C,D 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-ray10.32-0.90MULTICCDFRELON CCD CAMERA1.930.038.130.14.220.0910ID2ESRF GRENOBLE
neutron21.94COLETTEHE-3 ORDELA DETECTOR7.571LOQISIS RUTHERFORD- APPLETON LAB

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Processing

Software
NameVersionClassification
SCTPL7model building
GNOMmodel building
Insight IIII 98model building
COLETTE(ISIS)data scaling
SCTPL7phasing
GNOMphasing
RefinementMethod to determine structure: CONSTRAINED SCATTERING MODELLING
Details: THE COORDINATES CONTAIN ONLY CA ATOMS.
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 0 0 3395
Soln scatter modelNum. of conformers submitted: 10 / Representative conformer: 1 / Software list: INSIGHT II, SCTPL7, GNOM

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