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- PDB-2esg: Solution structure of the complex between immunoglobulin IgA1 and... -

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Basic information

Entry
Database: PDB / ID: 2esg
TitleSolution structure of the complex between immunoglobulin IgA1 and human serum albumin
Components
  • Immunoglobulin A1 heavy chain
  • Immunoglobulin A1 light chain
  • Serum albumin
KeywordsIMMUNE SYSTEM/TRANSPORT PROTEIN / immunoglobulin / antibody / human serum albumin / IMMUNE SYSTEM-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


maintenance of mitochondrion location / Transport of organic anions / protein metabolic process => GO:0019538 / secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / platelet degranulation / IgA immunoglobulin complex / high-density lipoprotein particle remodeling ...maintenance of mitochondrion location / Transport of organic anions / protein metabolic process => GO:0019538 / secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / platelet degranulation / IgA immunoglobulin complex / high-density lipoprotein particle remodeling / cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / retina homeostasis / negative regulation of programmed cell death / IgG immunoglobulin complex / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / positive regulation of respiratory burst / antioxidant activity / toxic substance binding / small molecule binding / Scavenging of heme from plasma / Recycling of bile acids and salts / immunoglobulin complex, circulating / immunoglobulin receptor binding / cellular response to starvation / post-translational protein modification / receptor-mediated endocytosis / platelet alpha granule lumen / complement activation, classical pathway / fatty acid binding / Cell surface interactions at the vascular wall / antigen binding / Post-translational protein phosphorylation / B cell receptor signaling pathway / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / antibacterial humoral response / adaptive immune response / blood microparticle / immune response / copper ion binding / endoplasmic reticulum lumen / negative regulation of apoptotic process / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Immunoglobulin ...Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Immunoglobulin / Immunoglobulin domain / 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 alpha 1 / Albumin / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING / SYNCHROTRON
AuthorsAlmogren, A. / Furtado, P.B. / Sun, Z. / Perkins, S.J. / Kerr, M.A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Purification, Properties and Extended Solution Structure of the Complex Formed between Human Immunoglobulin A1 and Human Serum Albumin by Scattering and Ultracentrifugation.
Authors: Almogren, A. / Furtado, P.B. / Sun, Z. / Perkins, S.J. / Kerr, M.A.
History
DepositionOct 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: 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 1.4Jun 13, 2018Group: Data collection / Category: diffrn_radiation
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_scattering_type
Revision 1.5Feb 14, 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 999SEQUENCE THE VH DOMAIN SEQUENCE (RESIDUES 1-122) IS THAT FROM THE HUMAN TR1.9 FAB STRUCTURE (CODE: ...SEQUENCE THE VH DOMAIN SEQUENCE (RESIDUES 1-122) IS THAT FROM THE HUMAN TR1.9 FAB STRUCTURE (CODE: 1VGE). THE LIGHT CHAIN SEQUENCE IS THAT FROM THE HUMAN TR1.9 FAB STRUCTURE (CODE: 1VGE).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Immunoglobulin A1 light chain
M: Immunoglobulin A1 light chain
A: Immunoglobulin A1 heavy chain
B: Immunoglobulin A1 heavy chain
C: Serum albumin


Theoretical massNumber of molelcules
Total (without water)215,1425
Polymers215,1425
Non-polymers00
Water00
1


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

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Components

#1: Antibody Immunoglobulin A1 light chain / Coordinate model: Cα atoms only


Mass: 23216.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Purified with Thiophilic chromatography and gel filtration from serum of a patient with IgA1 myeloma
Source: (natural) Homo sapiens (human) / Tissue fraction: serum
#2: Antibody Immunoglobulin A1 heavy chain / Coordinate model: Cα atoms only


Mass: 51068.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Purified with Thiophilic chromatography and gel filtration from serum of a patient with IgA1 myeloma
Source: (natural) Homo sapiens (human) / Tissue fraction: serum / References: UniProt: P01876*PLUS
#3: Protein Serum albumin / Coordinate model: Cα atoms only


Mass: 66571.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJZ0, UniProt: P02768*PLUS

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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
12781
22781
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SPALLATION SOURCEISIS INSTRUMENT LOQ12.0-10.0
SYNCHROTRONESRF ID221
Detector
TypeIDDetectorDate
3_He ORDELA1AREA DETECTORJul 1, 2001
CCD2CCDJul 1, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1TIME OF FLIGHTLAUELneutron1
2MIRRORSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
121
2101
311
Soln scatter

Data analysis software list: SCTPL7, GNOM / Num. of time frames: 1 / Sample pH: 7.4 / Source class: Y / Temperature: 288 K

TypeIDBuffer nameConc. 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)Protein lengthSource beamlineSource type
x-ray112.5 MM NA PHOSPHATE 140 MM NACL0.9-1.9MULTICCDFRELON CCD CAMERA1.310.057.470.312.310.111IDO2ESRF GRENOBLE
neutron212.5 MM NA PHOSPHATE 140 MM NACL 99.9% D2O1.2-1.9COLETTEHE-3 ORDELA DETECTOR7.090.1LOQISIS RUTHERFORD

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Processing

Software
NameVersionClassification
COLETTEdata reduction
SCTPL7model building
GNOMmodel building
Insight IIII 98model building
COLETTEdata scaling
SCTPLV. 7phasing
GNOMphasing
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 0 0 1956
Soln scatter modelNum. of conformers submitted: 1 / Software list: INSIGHT II, SCTPL7, GNOM

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