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- PDB-1w2s: Solution structure of CR2 SCR 1-2 in its complex with C3d by X-ra... -

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Basic information

Entry
Database: PDB / ID: 1w2s
TitleSolution structure of CR2 SCR 1-2 in its complex with C3d by X-ray scattering
Components
  • COMPLEMENT C3 PRECURSOR
  • COMPLEMENT RECEPTOR TYPE 2 PRECURSOR,
KeywordsIMMUNE SYSTEM / X-RAY SCATTERING / ANALYTICAL ULTRACENTRIFUGATION / COMPLEMENT / THROMBOSPONDIN TYPE I REPEATS / CONSTRAINED MODELLING / GLYCOPROTEIN / IMMUNOLOGY
Function / homology
Function and homology information


negative regulation of complement activation, classical pathway / complement receptor activity / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / complement binding / positive regulation of activation of membrane attack complex / T cell mediated immunity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance ...negative regulation of complement activation, classical pathway / complement receptor activity / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / complement binding / positive regulation of activation of membrane attack complex / T cell mediated immunity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of type IIa hypersensitivity / complement receptor mediated signaling pathway / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement activation / complement activation, alternative pathway / immunoglobulin receptor binding / endopeptidase inhibitor activity / neuron remodeling / type I interferon-mediated signaling pathway / amyloid-beta clearance / B cell activation / B cell proliferation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / Regulation of Complement cascade / B cell differentiation / response to bacterium / Post-translational protein phosphorylation / fatty acid metabolic process / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of protein phosphorylation / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / transmembrane signaling receptor activity / virus receptor activity / secretory granule lumen / G alpha (i) signalling events / blood microparticle / receptor complex / immune response / G protein-coupled receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / inflammatory response / signaling receptor binding / Neutrophil degranulation / symbiont entry into host cell / cell surface / signal transduction / protein homodimerization activity / protein-containing complex / extracellular space / DNA binding / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
: / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 ...: / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / : / Anaphylatoxin domain signature. / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C3 / Complement receptor type 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION SCATTERING
Model type detailsCA ATOMS ONLY, CHAIN A, B
AuthorsGilbert, H.E. / Hannan, J.P. / Holers, V.M. / Perkins, S.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Solution Structure of the Complex between Cr2 Scr 1-2 and C3D of Human Complement: An X-Ray Scattering and Sedimentation Modelling Study.
Authors: Gilbert, H.E. / Eaton, J.T. / Hannan, J.P. / Holers, V.M. / Perkins, S.J.
History
DepositionJul 8, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 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: COMPLEMENT C3 PRECURSOR
B: COMPLEMENT RECEPTOR TYPE 2 PRECURSOR,


Theoretical massNumber of molelcules
Total (without water)49,9912
Polymers49,9912
Non-polymers00
Water00
1


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

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Components

#1: Protein COMPLEMENT C3 PRECURSOR / C3D / Coordinate model: Cα atoms only


Mass: 34379.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET11B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P01024
#2: Protein COMPLEMENT RECEPTOR TYPE 2 PRECURSOR, / CR2 SCR 1-2 / COMPLEMENT C3D RECEPTOR / EPSTEIN-BARR VIRUS RECEPTOR / EBV RECEPTOR / CD21 ANTIGEN / Coordinate model: Cα atoms only


Mass: 15611.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P20023

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Data collection

Soln scatter
TypeIDBuffer nameConc. range (mg/ml)Data reduction software listDetector typeMean guiner radius (nm)Mean guiner radius esd (nm)Num. of time framesProtein lengthSource classSource typeTemperature (K)
x-ray110 MM HEPES, 50 MM NACL0.4-4.3MULTICCDFRELON CCD CAMERA2.440.119YESRF BEAMLINE ID02288
modelling2

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Processing

SoftwareName: INSIGHT / Version: II 98 / Classification: refinement
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms449 0 0 0 449
Soln scatter modelNum. of conformers submitted: 6 / Representative conformer: 1 / Software author list: MSI / Software list: INSIGHT II, SCTPL7, GNOM

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