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- PDB-2ocw: Solution structure of human secretory component -

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Basic information

Entry
Database: PDB / ID: 2ocw
TitleSolution structure of human secretory component
ComponentsPolymeric-immunoglobulin receptor
KeywordsIMMUNE SYSTEM / SC / Immunoglobulin / Secretory / Antibody / Immunity
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
AuthorsBonner, A. / Perrier, C. / Corthesy, B. / Perkins, S.J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Solution structure of human secretory component and implications for biological function.
Authors: Bonner, A. / Perrier, C. / Corthesy, B. / Perkins, S.J.
History
DepositionDec 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: 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
A: Polymeric-immunoglobulin receptor


Theoretical massNumber of molelcules
Total (without water)64,3551
Polymers64,3551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Number of models9

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Components

#1: Protein Polymeric-immunoglobulin receptor / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIGR / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): OVARIAN CELLS / References: UniProt: P01833

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 1 Å
DetectorType: CCD / Detector: CCD / Date: Dec 1, 2004 / Details: MIRRORS
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Soln scatter

Conc. range: 0.62-2.0 / Data analysis software list: SCTPL7, GNOM / Protein length: 1 / Source class: Y / Temperature: 288 K

TypeIDBuffer nameData reduction software listDetector typeMean 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 framesSample pHSource beamlineSource type
x-ray19.6 MM NA, K PHOSPHATE 116MM NACL 10.4MM NA2HPO4 3.2MM NAH2PO4MULTICCDFRELON CCD CAMERA3.530.031.760.08107.2IDO2ESRF GRENOBLE
neutron29.6 MM NA, K PHOSPHATE 2.7MM KCL 8.1MM NA2HPO4 1.5MM KH2PO4 99.9% D2OCOLETTEHE-3 ORDELA DETECTOR3.630.271.070.0717.5LOQISIS RUTHERFORD

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Processing

Software
NameVersionClassification
SCTPL7model building
GNOMmodel building
Insight IIII 98model building
COLETTE(ISIS)data scaling
SCTPLV. 7phasing
GNOMphasing
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms585 0 0 0 585
Soln scatter modelDetails: MODEL 1 CORRESPONDS TO OUR BEST FIT STRUCTURE IN THE PRIMARY REFERENCE. MODELS 2-10 CORRESPOND TO THE OTHER NINE MODELS THAT GAVE SIMILAR GOOD FITS TO THE X-RAY AND NEUTRON DATA.
Num. of conformers submitted: 10 / Representative conformer: 1 / Software list: INSIGHT II, SCTPL7, GNOM

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