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- PDB-2gsx: Complement Receptor Type 2 -

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Basic information

Entry
Database: PDB / ID: 2gsx
TitleComplement Receptor Type 2
ComponentsComplement receptor type 2
KeywordsIMMUNE SYSTEM / Complement / SCR domain / CCP domain / Sushi domain
Function / homology
Function and homology information


complement receptor activity / negative regulation of complement activation, classical pathway / T cell mediated immunity / complement binding / complement activation, alternative pathway / B cell proliferation / immunoglobulin receptor binding / complement activation, classical pathway / B cell differentiation / Regulation of Complement cascade ...complement receptor activity / negative regulation of complement activation, classical pathway / T cell mediated immunity / complement binding / complement activation, alternative pathway / B cell proliferation / immunoglobulin receptor binding / complement activation, classical pathway / B cell differentiation / Regulation of Complement cascade / transmembrane signaling receptor activity / virus receptor activity / receptor complex / immune response / protein homodimerization activity / DNA binding / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile.
Similarity search - Domain/homology
Complement receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING / SYNCHROTRON
AuthorsGilbert, H.E. / Asokan, R. / Holers, V.M. / Perkins, S.J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The 15 SCR Flexible Extracellular Domains of Human Complement Receptor Type 2 can Mediate Multiple Ligand and Antigen Interactions.
Authors: Gilbert, H.E. / Asokan, R. / Holers, V.M. / Perkins, S.J.
History
DepositionApr 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement receptor type 2


Theoretical massNumber of molelcules
Total (without water)104,3241
Polymers104,3241
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Number of models3

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Components

#1: Protein Complement receptor type 2 / Cr2 / Complement C3d receptor / Epstein-Barr virus receptor / EBV receptor / CD21 antigen / Coordinate model: Cα atoms only


Mass: 104323.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CR2, C3DR / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20023

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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
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF ID211
SPALLATION SOURCEISIS INSTRUMENT LOQ22.0, 10.0
Detector
TypeIDDetector
CCD1CCD
3-He ORDELA2AREA DETECTOR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSINGLE WAVELENGTHMx-ray1
2TIME OF FLIGHTLAUELneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
111
221
3101
Soln scatter

Data analysis software list: SCTPL7, GNOM / Mean guiner radius: 11.5 nm / Min mean cross sectional radii gyration: 1.8 nm / Min mean cross sectional radii gyration esd: 0.1 nm / Num. of time frames: 1 / Protein length: 1 / Source class: Y / Temperature: 288 K

TypeIDBuffer nameConc. range (mg/ml)Data reduction software listDetector typeMean guiner radius esd (nm)Sample pHSource beamlineSource type
x-ray19.6 MM NA, K PHOSPHATE 137 MM NACL 2.7 MM KCL 0.5 MM EDTA0.9-1.9MULTICCDFRELON CCD CAMERA0.97.5IDO2ESRF GRENOBLE
neutron29.6 MM NA, K PHOSPHATE 137 MM NACL 2.7 MM KCL 0.5 MM EDTA 99.9% D2O1.2-1.9COLETTEHE-3 ORDELA DETECTOR0.57.4LOQISIS RUTHERFORD

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Processing

Software
NameVersionClassification
COLETTE(ISIS)data reduction
SCTPL7model building
GNOMmodel building
Insight IIII 98model building
COLETTE(ISIS)data scaling
SCTPLV. 7phasing
GNOMphasing
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 0 0 951
Soln scatter modelDetails: THE ENTRY CONTAINS CA ATOMS ONLY.MODEL 1 REPRESENTS A LONGER MODEL FOR CR2 THAT BEST FITS THE RG VALUE. MODEL 2 REPRESENTS A MORE COMPACT MODEL FOR CR2 THAT BEST FITS THE SCATTERING DATA AT ...Details: THE ENTRY CONTAINS CA ATOMS ONLY.MODEL 1 REPRESENTS A LONGER MODEL FOR CR2 THAT BEST FITS THE RG VALUE. MODEL 2 REPRESENTS A MORE COMPACT MODEL FOR CR2 THAT BEST FITS THE SCATTERING DATA AT LARGE ANGLE. MODEL 3 REPRESENTS AN INTERMEDIATE MODEL THAT GIVES THE OVERALL BEST FIT TO THE SCATTERING DATA AND IS THE FINAL MODEL. SEE THE PRIMARY REFERENCE.
Num. of conformers submitted: 3 / Representative conformer: 1 / Software list: INSIGHT II, SCTPL7, GNOM

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