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- PDB-2rcj: Solution structure of human Immunoglobulin M -

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Basic information

Entry
Database: PDB / ID: 2rcj
TitleSolution structure of human Immunoglobulin M
Components
  • IgA1 heavy chain
  • IgA1 light chain
  • J chain
KeywordsIMMUNE SYSTEM / polymeric antibodies / immunology / constrained modelling
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
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
Immunoglobulin heavy constant gamma 1 / Hepatitis B virus receptor binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING
AuthorsPerkins, S.J. / Nealis, A.S. / Sutton, B.J. / Feinstein, A.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Solution structure of human and mouse immunoglobulin M by synchrotron X-ray scattering and molecular graphics modelling. A possible mechanism for complement activation.
Authors: Perkins, S.J. / Nealis, A.S. / Sutton, B.J. / Feinstein, A.
#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.
History
DepositionSep 20, 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 1.3Sep 23, 2020Group: Structure summary / Category: entity / struct_keywords / Item: _entity.pdbx_description / _struct_keywords.text
Revision 1.4Feb 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
A: IgA1 light chain
B: IgA1 light chain
C: IgA1 heavy chain
D: IgA1 heavy chain
E: IgA1 light chain
F: IgA1 light chain
G: IgA1 heavy chain
H: IgA1 heavy chain
I: IgA1 light chain
J: IgA1 light chain
K: IgA1 heavy chain
L: IgA1 heavy chain
M: IgA1 light chain
N: IgA1 light chain
O: IgA1 heavy chain
P: IgA1 heavy chain
Q: IgA1 light chain
R: IgA1 light chain
S: IgA1 heavy chain
T: IgA1 heavy chain
U: J chain


Theoretical massNumber of molelcules
Total (without water)809,95321
Polymers809,95321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
DetailsThis structure is a pentamer structure with 4 chains in each subunit - plus an additional J Chain to make it 21 polypeptide chains.

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Components

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


Mass: 23165.770 Da / Num. of mol.: 10 / Source method: isolated from a natural source
Details: Human immunoglobulin M was purified from the serum of a patient with Waldenstrom's disease
Source: (natural) Homo sapiens (human) / References: UniProt: Q6PYX1*PLUS
#2: Antibody
IgA1 heavy chain / Coordinate model: Cα atoms only


Mass: 56759.504 Da / Num. of mol.: 10 / Source method: isolated from a natural source
Details: Human immunoglobulin M was purified from the serum of a patient with Waldenstrom's disease
Source: (natural) Homo sapiens (human) / References: UniProt: P01857*PLUS
#3: Protein J chain / Coordinate model: Cα atoms only


Mass: 10700.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Human immunoglobulin M was purified from the serum of a patient with Waldenstrom's disease
Source: (natural) Homo sapiens (human)

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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
12931
22931
Diffraction source
TypeIDWavelength (Å)
OTHER11.54
OTHER21.54
Detector
TypeIDDetectorDate
300-Channel1LINEAR DETECTORJan 1, 1989
500-channel2QUADRANT DETECTORJan 1, 1989
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSINGLE WAVELENGTHMx-ray1
2MIRRORSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Soln scatterType: x-ray / Buffer name: 200 MM NACL 12 MM NAHPO4 0.05% NA AZIDE / Conc. range: 2-30 / Data analysis software list: SCTPL2 / Data reduction software list: SWANAL / Detector type: LINEAR DETECTOR / Max mean cross sectional radii gyration: 1.79 nm / Max mean cross sectional radii gyration esd: 0.12 nm / Mean guiner radius: 12.17 nm / Mean guiner radius esd: 0.34 nm / Min mean cross sectional radii gyration: 6.06 nm / Min mean cross sectional radii gyration esd: 0.19 nm / Num. of time frames: 1 / Sample pH: 7 / Source beamline: 7.3 / Source class: Y / Source type: SRS DARESBURY / Temperature: 293 K

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Processing

Software
NameClassification
SCTPL2model building
FRODOmodel building
Insight IImodel building
SWANALdata scaling
OTOKOdata scaling
SCTPL2phasing
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms7514 0 0 0 7514
Soln scatter modelDetails: THE DEPOSITED STRUCTURE CONTAINS ONLY CA ATOMS. THE IGM COORDINATES ARE PROVIDED FROM AN EARLY STUDY IN WHICH A MANUAL FIT METHOD BASED ON KNOWN CRYSTAL STRUCTURES FOR IGG WAS USED TO ...Details: THE DEPOSITED STRUCTURE CONTAINS ONLY CA ATOMS. THE IGM COORDINATES ARE PROVIDED FROM AN EARLY STUDY IN WHICH A MANUAL FIT METHOD BASED ON KNOWN CRYSTAL STRUCTURES FOR IGG WAS USED TO DETERMINE STRUCTURES FOR INTACT IGM AND ITS FAB, FAB'2, FC5 AND IGM-S MONOMER SUBUNITS. THESE CRYSTAL STRUCTURES ORIGINATED FROM HUMAN FAB KOL (PDB CODE 2FB4) AND HUMAN FC (PDB CODE 1FC1). THIS PROCEDURE IS APPROXIMATE AND THE IGM MODEL IS NOT CONSIDERED TO BE OPTIMAL OR REFINED AGAINST THE X-RAY SCATTERING DATA.
Num. of conformers submitted: 1 / Software list: FRODO, INSIGHT, SCTPL2

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